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GenePilot v1.0b

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1. Yellow Blue Palete gt Yellow Blue Default This selection selects the traditional colors of Yellow and Blue for the heatmap Yellow is positive or Correlated and Blue is negative or Anti Correlated Select Heatmap Palette Gray Scale Palette gt Gray Scale This selection selects shades of gray for the heatmap Light Gray is positive or Correlated and Dark Gray is negative or Anti Correlated 42 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Create Dataset Interface Show Palette Palette gt Show Palette This selection Launches the Palette Window which shows the color palette used by the heatmap Show Rows Normalized Normalize gt Norm This selection changes the heatmap to show each row normalized That means that the color corresponding to the highest value in the palette will be applied to the highest value in the row the color corresponding to the lowest value in the palette will be applied to the lowest value in the row and all other values will be scaled accordingly Show Rows Un Normalized Normalize gt NoNorm This selection displays the traditional heatmap display where color selections from the palette are determine from the highest and lowest value among the data not just in a row Url Targets for Row Fields Interface File gt Preferences gt Field Info Urls This selection launches the preferences window for Field Info Target Url Interface Create Dataset BE create Dotnet from NCI PMA T ENTA
2. Button Select Top This button selects the Gene Ontologies that are at the top of the list in the quantity specified Button Unselect All This button unselects all of the currently selected Gene Ontologies Button Save Changes This button sets the currently selected settings and closes the window Button Cancel This button closes the window without setting any of the changes made 87 GenePilot V 1 07b August 28 2003 SAM Copy to File Clipboard Interface Copy to Clipboard Bi Cory Lo Chpheoard information xi Description Copy to Clipboard Interface This Interface allows the user to select which Row Information Fields to include in the Copy to Clipboard and to specify the rows that they want 5 alerted Eng O Aot included in the selection Sebo Fio Inf orsoraes Fonds 0 anche Ciona Ms Select how much data to copy EH rymicel LseusLink is This section determines which rows will be selected When All Rows is selected then all of the rows in the current delta range are copied to the clipboard When Selected Rows is selected then only the selected rows will be included unless there are no selected rows in which case all the Uei rara Ham 7 dumini Function Gene Gripp anneta R pkentutn mi Aes rows in the current delta will be included Repriaentutes Prowin Acc Linien Cola ir Select Row Information Fields to include Comto Cipboard Canet This section allows the us
3. Class Vector Name If the vector is a classification Vector then it will be in this menu If multiple runs were selected then each class will also be included in the menu so that each run can be viewed If the Vector was a Shape Vector but there are classification Vector s available then they will be selectable for being used to indicate classes for the columns 82 GenePilot V 1 07b August 28 2003 SAM Menu Choices Select Heatmap Palette Red Green Palette gt Red Green This selection selects the traditional colors of Red and Green for the heatmap Red is positive or Correlated and Green is negative or Anti Correlated Select Heatmap Palette Yellow Blue Palete gt Yellow Blue Default This selection selects the traditional colors of Yellow and Blue for the heatmap Yellow is positive or Correlated and Blue is negative or Anti Correlated Select Heatmap Palette Gray Scale Palette gt Gray Scale This selection selects shades of gray for the heatmap Light Gray is positive or Correlated and Dark Gray is negative or Anti Correlated Show Palette Palette gt Show Palette This selection Launches the Palette Window which shows the color palette used by the heatmap Show Rows Normalized Normalize gt Norm This selection changes the heatmap to show each row normalized That means that the color corresponding to the highest value in the palette will be applied to the highest value in the row the color corresponding to th
4. mrn Sem cogens concu in Gene Ontology Settings Panel This selection sets the Gene Ontology Categories to Display with the following options Biological Process Shows only Biological Process Cellular Component Shows only Cellular Component Biological Process amp Cellular Component Shows both Categories Molecular Function Shows only Molecular Function Biological Process amp Molecular Function Shows both Categories Cellular Component amp Molecular Function Shows both Categories AII Shows all three Categories Select control for Gene Ontology Columns This selection sets the way that Gene Ontology Columns are selected with the following options Auto Selection Chooses most common Gene Ontologies among selected rows if avail then fills in remaining if necessary from most common among remaining rows Auto Set Chooses most common Gene Ontologies among displayed rows User Select Displays rows that the user has specifically selected This gets turned off when the user clicks on the Gene Ontology Names 27 GenePilot V 1 07b August 28 2003 Dataset Display Gene Ontology Preferences Select or View Gene Ontology Entries This section is for viewing or selecting specific Gene Ontologies by checking the checkbox either manually or using the Select Top button under the list List Show Choices This selection sets the Gene Ontologies that will be displayed in the list for selection It has t
5. 1 Clicking and dragging on the bitmap will select those rows 2 Holding down the shift key and selecting a row will extend the row from the previous selection down to the selected row This can be used to select rows in a group that is larger than those seen on the screen 80 GenePilot V 1 07b August 28 2003 SAM Menu Choices Results Menu Choices Bitmap from All Action gt Save All to Bitmap This selection creates a gif bitmap containing all of the information in the Lower Panel Bitmap from Graphs Action gt Graph to Bitmap This selection saves the two graphs FDR and Score Plot to a gif bitmap Bitmap from Selected Action gt Save Sel to Bitmap This selection creates a gif bitmap containing all of the information in the Lower Panel If rows are selected then only the selected rows will be included in the bitmap If no rows are selected then all of the rows in the current Delta are saved to the bitmap Copy to Clip Action gt Copy to Clip This selection launches an interface for copying all or selected rows to the clipboard This interface also allows for selecting the Row Information Fields which the user is interested in Copy to File Action gt Copy to File This selection launches an interface for copying all or selected rows to a file This interface also allows for selecting the Row Information Fields which the user is interested in Create Vector Action gt Create Vector This selection launches the Create Vector dial
6. Description The Row Information Page is an html page that is generated by GenePilot It includes a hashtable showing the relationships between the selected genes and the Gene Ontology Categories when Gene Ontology information is imported or loaded all of the Row information for each of the currently selected rows and links to more information from the fields that are configured to have links using Preferences gt Set Links The purpose of this page is to provide maximum information for selected genes in a format that can be easily emailed toa colleague EET era TENET H I Gene Ontology Hashtable This image which has the same prefix as the webpage contains a hashtable of up to 50 of the most common Gene Ontologies with circles in the rows that they are included in Clicking on the row description same description as set by the user for Row Information will take the user to the full description of known information contained within GenePilot Row Information Each Row among the selected rows will have it s own information section in this html page Within this section will be displayed all of the information that has been loaded into GenePilot for this Row Also within this section will be links to additional information if there is information that has a valid link set Additional information The image at the top when there is Gene Ontology Information has the same name ending in gif as the html page This is
7. Gene Ontology Names Middle Right If Gene Ontology Information The Gene Ontology Names is a variable column display that displays the Gene Ontology Names that are currently chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set If specific Gene Ontologies are selected by the user the settings can be easily changed back to automatic selection by clicking on this Gene Ontology Names display Gene Ontology Indication Bottom Middle The Gene Ontology Indication indicates the Gene Ontologies that are associated with each row The Gene Ontologies are chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set Row Information Bottom Right Row information contains the row name and row information to the right of each row in the heatmap Row Information Bottom Right Row information contains the row name and row information to the right of each row in the heatmap Class Information Top Right If Class Vector If there is Classification Vector s there will be Class Information which defines the color coding for the Class Indication row Actions 1 Clicking and dragging on the bitmap will select those rows 66 GenePilot V 1 07b August 28 2003 SOM Menu Choices 2
8. Missing Data Imputation 16 Nearest Neighbor 16 N Nearest Neighbor 16 Neighborhood Type SOM 63 New Dataset Make Template 13 Node Panel SOM 64 Normalize Row Hierarchical Clustering 43 Normalize Rows Dataset Display 25 K Means Clustering 55 SAM 83 SOM 69 Number of Clusters K Means Clustering 50 O Original Data Show 25 94 GenePilot V 1 07b August 28 2003 Index Pairs Vector Creating Dataset Templates 7 Palette 31 Palette Show Dataset Display 25 Pre Process Settings View 13 Preparing Data 8 Classification Vector 10 Column Names 9 Data Header 10 Data Rows 11 Dataset Name 8 Information 9 Lead Col Count 9 Model Number 9 Pair Data Vector 10 Replicates Vector 9 Shape Vector 10 Type of Data 8 Vectors 10 Q Quit 13 R Replicate Column Combine Panel 18 Column and Row Statistics Display 19 Mean Value 19 Median Value 19 Set Description 19 Set Name 19 Weighted Mean Value 19 Replicate Column Vector Add to Template 6 Representative mRNA Acc Creating Dataset Templates 7 Representative Protein Acc Creating Dataset Templates 7 Results Launching Row Info Display 14 Row Info Display Dataset Display 24 26 Hierarchical Clustering 44 K Means Clustering 57 Launching settings interface 14 SAM 85 SOM 71 Row Info Import 17 Row Information Hierarchical Clustering 40 K Means Clustering 53 66 SAM 80 SOM 66 Row Information Page 32 Row Information Window 31 33 Row Similarity Metric 36 Row Type Cr
9. Heatmap Panel It io TE UE Melenoma m R S8 ae BLung Cancer Ce Cee ET Eget IMENS uil PEANG peas es SColon Ce ccce mA ME E Ovarian i i ui uj j ui id li tu u qas Se LB o a Oa moestSomt BRenal O ay cms m O ESTs Moderately similar ta Kren M musc BU sntiquitin A 024017 3 Aaoe4orsy BO 0 ESTs Bb 3 An 3anza 9 L 0 F00 O Tight junction protein 1 zona occludens BU Cyelin dependentkinase inhibitor 2A mel O BO 0 ESTs Chr 588190 hi 5 A5057287 3 B MAJOR GASTROINTESTINAL TUMDR A B ESTs 5 3 N20008 BO 0 ANN Annexin III lipaeartin IIT Chr d 325 BENHBNHEO CAbLD1Caldesmon Che 486474 EW Homo sapiens serum inducible kinase mR BENBNHE Caldesmon 5 H51958 3 H52087 SAM Heatmap Panel 1 Heatmap 2 Class Indicator 3 Column Information 4 Gene Ontology Indicator 5 Gene Ontology Names 6 Correlation Indicator and FDR 7 Row Information 8 Class Information Description This panel contains the specific information for the rows or clusters The central part is the Heatmap which contains colors from the Palette to indicate values of each row or cluster To the top of each column is the Column Info in the form of text rotated counter clockwise by 90 degrees A row of rectangles which are color coded to indicate the class of each column will be in between the Heatmap and the Column Info when Classification Vector s are available To the right of the Heat
10. and Green lowest value When No Normalize is selected the value range is defined by the min and max values in the entire Dataset Rows remaining after filtering with zero being the medium value When Normalize is selected then the value range for each row is defined by the min and max values in that row with the mean value being the medium value Average Heatmap Above Heatmap The Average Heatmap is a single rowed version of the Heatmap It represents the average vector for the current cluster 39 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Results Menu Choices Class Indication Above Average Heatmap If there is Classification Vector s there will be Class Indicators above the Average Heatmap This is a row of rectangles which are color coded to indicate the class of each column as defined by the Class Information block in the Top Right corner Column Names Upper Left The Column Information contains the column names rotated counter clockwise by 90 degrees above each column in the Heatmap Column Dendigram Top Left If Column Clustering Selected If Column clustering has been selected there will be a dendigram at the top If there is a Category Vector for this dataset the top dendigram will be color coded by class The column dendigram displays the cluster tree of the columns Similar columns are clustered together with either another column or a cluster depending on which is closer Distances can be
11. AE M Description Create Sub Dataset Interface This Interface is used to create anew Dataset by using Set Hew Dataset Mame Ho Tmar 1375 be a cluster or selected text within a cluster for defining Set Columns to inckode Deika Saia Cobar either the rows in the new dataset or the rows to be Set how Datusot info excluded in the new Dataset Ganarates rom he ROI T Maire 1 376 Set New Dataset Name x This text field is the name that the new Dataset will Sut Whether Da Include or Excduda Saleciiena receive Itis seeded with the result Dataset Name khe UG Exe C along with HC to indicate that it was created using the results from a Hierarchical Clustering result screen ff Up Cumt Selected Fieri That name can bet set to anything as long as the name C Mee Cum Cheer is not already in the system Crate Date Cancer Heie Create Dataset Settings Window Select Columns to Include Default All The button Select Columns launches a window that allows for selection of the columns to be included in the new Dataset If no column selection is made then all columns will be used Set New Dataset Info This text field is the Dataset information field It is seeded from the result Dataset Information Additional information should be added here to provide a pedigree for the new Dataset 43 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Row Info Display Settings Set Whether to Include or Exclude Selections When In
12. August 28 2003 Chapter 7 Omni SAM Description SAM is asupervised method for finding significant rows in a MicroArray It requires Vector information in the form of either a Classification Vector or a Shape Vector Using the information contained in one of these vectors SAM ranks rows according to their significance to the Vector In the case of Shape Vectors rows whose vector has a shape similar to the Shape Vector or it s mirror image will have greater significance resulting in a lower FDR than those rows will less resemblance to the Shape Vector In the case of Classification Vectors Rows which have similar values in columns of the same class and these similar values are distinct from columns of other classes have greater significance resulting in a lower FDR than those rows with less cohesion within a class An option that is available for Classification Vectors is to add additional runs where each class is compared against all other classes This helps find rows where values in one class are similar and the values of this class are distinct from the rest of the values The result screen is made up of three panels The FDR Graph Panel plots the FDR against the percentage of rows The Score Graph Panel plots the score against the expected score The Heatmap Panel displays the Heatmap and other related information for the significant rows as selected by the Delta Slider on the top For more information o
13. Component Shows only Cellular Component Biological Process amp Cellular Component Shows both Categories Molecular Function Shows only Molecular Function Biological Process amp Molecular Function Shows both Categories Cellular Component amp Molecular Function Shows both Categories All Shows all three Categories 58 GenePilot V 1 07b August 28 2003 K Means Clustering Gene Ontology Preferences Select control for Gene Ontology Columns This selection sets the way that Gene Ontology Columns are selected with the following options Auto Selection Chooses most common Gene Ontologies among selected rows if avail then fills in remaining if necessary from most common among remaining rows in the cluster Auto Set Chooses most common Gene Ontologies among the rows of the current cluster User Select Displays rows that the user has specifically selected This gets turned off when the user clicks on the Gene Ontology Names Select or View Gene Ontology Entries This section is for viewing or selecting specific Gene Ontologies by checking the checkbox either manually or using the Select Top button under the list List Show Choices This selection sets the Gene Ontologies that will be displayed in the list for selection It has the following choices Show All GO Displays all of the Gene Ontologies that are associated with the current Dataset Show only GO from Cluster Displays the Gene Ontologies that are associated with gen
14. Holding down the shift key and selecting a row will extend the row from the previous selection down to the selected row This can be used to select rows in a group that is larger than those seen on the screen 3 When user selected gene ontologies are displayed the Gene Ontology displays can be reverted back to automatic mode by clicking on the Gene Ontology Names Results Menu Choices Bitmap from All Action gt Save All to Bitmap This selection creates a gif bitmap containing all of the information in the Lower Panel Bitmap from Grid Action gt Graph to Bitmap This selection saves the current node grid to a gif bitmap Bitmap from Selected Action gt Save Sel to Bitmap This selection creates a gif bitmap containing all of the information in the Lower Panel If no nodes are selected the bitmap will contain the node vector heatmap If a node is selected and rows are selected then only the selected rows will be included in the bitmap If a node is selected and no rows are selected the entire contents of the lower panel will be included in the bitmap Copy to Clip Action gt Copy to Clip This selection launches an interface for copying all or selected rows to the clipboard This interface also allows for selecting the Row Information Fields which the user is interested in Copy to File Action gt Copy to File This selection launches an interface for copying all or selected rows to a file This interface also allows for selecting the Row
15. Search 42 48 Search Again 42 Select Palette 42 Show Palette 43 Import Load Dataset Archive 13 Importing Additional Row Info 17 Info Page 93 GenePilot V 1 07b August 28 2003 Index Dataset Display 24 Hierarchical Clustering 41 K Means Clustering 54 SAM 82 SOM 68 Installation 2 All Other Platforms Instructions 4 Generic Unix Instructions 3 HP UX Instructions 3 Linux Instructions 3 Mac OS Classic 8 1 or greater Instructions 2 Mac OS X Instructions 2 Solaris Instructions 3 Windows Instructions 2 K K Means Clustering 49 Bitmap 53 Copy to Clipboard 54 Copy to Clipboard Interface 60 Copy to File 54 Copy to File Interface 60 Create Dataset 56 Create Vector 54 Field Info Url Targets Interface 56 Gene Ontology 53 66 Gene Ontology Display Settings 54 Gene Ontology Settings 58 Gene Ontology Statistics 54 Graph 50 Graph and Button Panel 50 Heatmap Panel 52 Launch Info Page 54 Normalize Rows 55 Palette 31 Quit 54 Row Info Display 57 Row Information Page 32 Row Information Window 31 33 Run 14 Run Settings 50 Save Results 55 Search 55 61 Select Palette 55 Show Palette 55 Linear Calibration 15 Linkage Measure 36 Load Dataset Archive 13 LocusLink ID Creating Dataset Templates 7 M Main Window 12 21 Description 12 21 Menu Choices 13 Make Dataset Dataset Display 24 Hierarchical Clustering 42 K Means Clustering 54 SAM 82 SOM 68 Make Template Dataset 13 Mean Centering 15 Median Centering 15
16. Studies Reference 5 A Sturn 62 GenePilot V 1 07b August 28 2003 SOM Run Settings Run Settings Grid size in columns 5 Description Grid size in rows s The Run Settings provide a means to alter the way that SOM analyzes the Data It is recommended SSS that the default settings are used at first then to try Grid Type Square ka out the other settings to view other results Because SOM is randomly seeded initially each run even Aaker o Hera fioo with the same settings will result in unique results It may therefore be useful to try several runs on a new Dataset to see what type of results can be Neighborhood Type Gaussian yielded Grid size in columns Initial Size of Neighborhood 3 This selection determines the number node columns paket initial Seed Type Random Rows Grid size in rows This selection determines the number of node rows Run Reset View Saved Result that will be used SOM Run Settings Menu Grid Type This selection determines the type of grid that will be used 1 Square each node is in the shape of a square and has 8 adjacent nodes 2 Hexagon each node is in the shape of a hexagon and has 6 adjacent nodes Number of Iterations This selection determines the number of times that a row vector is randomly selected then fit into the grid The number selected should be at least 10 times the number of rows Neighborhood Type This determines the di
17. all rows are used to fill in the categories Specific Gene Ontology categories can also be specified this is aided by the List Show Choices and List Order Choices for quickly finding specific Gene Ontologies Select Number of Gene Ontology Columns to show This selection sets the number of columns that will be displayed Select GO Types in Display re toa Setings x Gane Ontelegy Settings Paral Sebel Murnbeer of Gores Ontology Columm taster UNE Geto G0 Type dio Debs plos ae Sell conn E kai telecine C Ag Gija C User Select Saskect on Vinos Corus Orel ire Unirii List Shoe Choices eure enis CH Brie belt List Order Choices 1508 Es her Shy Gane Onioioge Mame Chester qi E ieisgra te plat mamsrase t4 signal transduction ta O isieaciliolar space s 2 Saied Tos Unsetect As sew canes cone so Gene Ontology Settings Panel This selection sets the Gene Ontology Categories to Display with the following options Biological Process Shows only Biological Process Cellular Component Shows only Cellular Component Biological Process amp Cellular Component Shows both Categories Molecular Function Shows only Molecular Function Biological Process amp Molecular Function Shows both Categories Cellular Component amp Molecular Function Shows both Categories All Shows all three Categories 45 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Gene Ontology
18. allows the user to search the rows for a String See Search Interface for more information on the Search Interface 24 GenePilot V 1 07b August 28 2003 Dataset Display Dataset Menu Choices Search Again Action gt Search Again This selection searches for the next case of the search string using the settings from the previous search Select Classification Vector If Avail Classes gt Class Vector Name If there is one or more Classification Vectors then one of those vectors can be selected for class indication of columns in either the Column Dendigram if column clustering was selected or the Class Indicator in the Right Panel Select Heatmap Palette Red Green Palette gt Red Green This selection selects the traditional colors of Red and Green for the heatmap Red is positive or Correlated and Green is negative or Anti Correlated Select Heatmap Palette Yellow Blue Palete gt Yellow Blue Default This selection selects the traditional colors of Yellow and Blue for the heatmap Yellow is positive or Correlated and Blue is negative or Anti Correlated Select Heatmap Palette Gray Scale Palette gt Gray Scale This selection selects shades of gray for the heatmap Light Gray is positive or Correlated and Dark Gray is negative or Anti Correlated Show Palette Palette gt Show Palette This selection Launches the Palette Window which shows the color palette used by the heatmap Show Rows Normalized Normalize gt
19. avail 6 Row Information 7 Class Information when avail Description This panel contains information about the rows The central partis the Heatmap which contains colors from the Palette to indicate values of each row or cluster When Classification Vector s are available a Class Indication row which indicates the classes of each column above the Average Heatmap At the top is the Column Info in the form of text rotated counterclockwise by 90 degrees To the right of the Heatmap is the Gene Ontology indication when Gene Ontology information has been imported into GenePilot for this Dataset To the right is the Row Information which contains the description of the row In the top right corner the legend for the Class Indication will define the colors for each class when Classification Vector s are available Heatmap Bottom Left The heatmap contains rectangles color coded in the Palette colors to represent the value of each cel juncture of 1 row and 1 column By default these colors are Red highest value and Green lowest value When No Normalize is selected the value range is defined by the min and max values in the entire Dataset Rows remaining after filtering with zero being the medium value When Normalize is selected then the value range for each row is defined by the min and max values in that row with the mean value being the medium value Class Indication Above Heatmap If there is Classification Vector s there
20. form of text rotated counter clockwise by 90 degrees To the right of the Heatmap is the Gene Ontology indication when Gene Ontology information has been imported into GenePilot for this Dataset To the rightis the Row Information which contains the description of the row In the top right corner the legend for the Class Indication will define the colors for each class when Classification Vector s are available When All Clusters is selected this Panel will contain information about the average vectors of each cluster When a cluster is selected then this panel will contain information about each row in that cluster sorted in the order of the closest correlated for to the cluster average vector to the furthest Heatmap Bottom Left The heatmap contains rectangles color coded in the Palette colors to represent the value of each cel juncture of 1 row and 1 column By default these colors are Red highest value and Green lowest value When No Normalize is selected the value range is defined by the min and max values in the entire Dataset Rows remaining after filtering with zero being the medium value When Normalize is selected then the value range for each row is defined by the min and max values in that row with the mean value being the medium value Class Indication Above Average Heatmap If there is Classification Vector s there will be Class Indicators above the Heatmap This is a row of rectangles which are color code
21. more convenient to turn off selection of most or all of the nodes Button Create Dataset This button creates the Dataset once all of the settings are made Button Cancel This button closes this interface without creating the new Dataset Preferences Row Info Display mmm x Raw Info Field Selection Paral Description Sect masque oe chai The Row Info Display Preferences Window is used to specify the Row Information fields that will be displayed to the right of the Heatmap In addition to selecting the fields the field order can be specified Se along with the character seperating the contents ofeach 77 field Fields are selected for inclusion by moving them from the left column Available over to the right Feepensantatve mRNA Acc column Included The order of display is set by their Foepeesentafive Protein Ac row order with the first row being the first display field 9 cusero Lish Para Gare Onfologs Aenelations Select separator char This selection sets the character that will separate the information from each field Row Info Field Selection Panel Select Row Info Fields This section allows for selection of the specific fields that will be displayed in the row info and the order of these fields It has the following buttons gt gt This button moves the currently hilited field in the left column over to the right column This button moves the currently hilited field in the right column over t
22. the search to be case sensitive Button Search This Button activates the search Button Cancel This button closes the interface without searching 89 GenePilot V 1 07b August 28 2003 References References References 1 SAM Reference Virginia Tusher Robert Tibshirani and Gilbert Chu 2000 Significance analysis of microarrays applied to the ionizing radiation response PNAS 2001 98 5116 5121 Apr 24 2 Good Paper on various clustering methods 1999 Tibshirani R Hastie T Eisen M Ross D Botstein D and Brown P Clustering methods for the analysis of DNA microarray data Tech report Oct 1999 3 Good paper on Hierarchical Clustering Eisen MB Spellman PT Brown PO and Botstein D 1998 Cluster Analysis and Display of Genome Wide Expression Patterns Proc Natl Acad Sci U S A 95 14863 8 4 Very good cluster Analysis Paper Sturn A Quackenbush J Trajanoski Z Genesis 2002 Cluster analysis of microarray data Bioinformatics 2002 Jan 18 1 207 8 5 Best paper on Clustering that I had seen up to that date Alexander Sturn Master Thesis 2001 Institute for Biomedical Engineering Graz University of Technology Graz Austria Cluster Analysis for Large Scale Gene Expression Studies 90 GenePilot V 1 07b August 28 2003 Index Index A Adjusted Data Show 25 Archive Dataset 13 Average Heatmap Hierarchical Clustering 39 B Bitmap from All Dataset Display 23 Hie
23. to make it easy to either save the page for later viewing or to send the pair to a colleague for their viewing 32 GenePilot V 1 07b August 28 2003 Dataset Display Url Loolup Editor Common Interfaces Url Lookup Editor Description The Url Lookup Editor provides a means to set Lookup Urls for Row Info Fields It is broken into two parts The Row Info Field Lookup Editor which sets a Lookup Url to a Row Info Field The Create Edit Lookup Url s section which adds new Urls that can then be assigned to a Row Info Field Current Row Info Field This selection sets the current Row Info Field Current Lookup name This selection contains a list of the Lookup s that are available for the current Row Info Field When a Row Info Field is first set it displays the current Lookup selected for the current Row Info Field To Change the set Lookup for a Row Info Field select a different Lookup then click on the Save Current Lookup Choice button Current Lookup Path This text field displays the actual Url for the currently selected Lookup Button Save Current Lookup Choice FE teckup Un belt teberace Ree Infe Field Lookup Editer Current Lookup Name Current Lookup unt hip ite epacty eric ge iniri eranc de Mlle awe Cume Lookup Choice Reset saved Lookup Choice essi reg I Crexte Edit Target Loekup s Solel Lookup to dg cr Create phew ESTEE Woe ce ba ie nt er et Re DH pg esi m S
24. will be Class Indicators above the Average Heatmap This is a row of rectangles which are color coded to indicate the class of each column as defined by the Class Information block in the Top Right corner Column Names Upper Left The Column Information contains the column names rotated counterclockwise by 90 degrees above each column in the Heatmap 22 GenePilot V 1 07b August 28 2003 Dataset Displa Dataset Menu Choices Gu aE To a eee The Gene Ontology Names is a variable column display that displays the Gene Ontology Names that are currently chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set If specific Gene Ontologies are selected by the user the settings can be easily changed back to automatic selection by clicking on this Gene Ontology Names display Gene Ontology Indication Bottom Middle The Gene Ontology Indication indicates the Gene Ontologies that are associated with each row The Gene Ontologies are chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set Row Information Bottom Right Row information contains the row name and row information to the right of each row in the heatmap Class Information Top Right If Class Vector If there is Class
25. Changes This button must be clicked in order for the changes to be made Button Cancel This button cancels any changes that were made and closes the window 26 GenePilot V 1 07b August 28 2003 Dataset Display Gene Ontology Preferences Preferences Gene Ontology Description This interface is used to set the Gene Ontology preferences for this screen The choices include automatic selection of the most common Gene Ontology categories based upon either the currently selected rows or for all rows If the selected rows have preference and there aren t enough categories to fill the number of columns then the most common categories across all rows are used to fill in the categories Specific Gene Ontology categories can also be specified this is aided by the List Show Choices and List Order Choices for quickly finding specific Gene Ontologies Select Number of Gene Ontology Columns to show This selection sets the number of columns that will be displayed Select GO Types in Display B ore Ooiskeey Settings Gana Ontalegy Settings Panal Shin Mumbar ii Gore Onion Colum D sheer i SeeciGOTwesinDiplak er Taai oni Acts Gelecios C7 ag Ciia CC User Select sisti inve aras Drel ile Unitrin List Shaw Choices List Order Choices oa Es Ler ety Gane Ontologe Hame 4C ester qi ieisgeai ie plage mamsrase 4 sigealtransducSentt d icer space s pam meman cosin E iae pt wiraciliciar airi
26. Dataset Information 6 amp Column Mames Vector Type Vector Name Colamed ColNamet Colame2 ColMames Class Vector Cancer 9 Breast Lung X Melenoma Lung Shape vector name19 1 03 0 2 0 8 1 5 Pair Vector name o 1 2 3 2 amp clonelD Clone ll Mizc Misc or Cv veight Leave val val val val 218522 Human brain mE homologe 4 67897 Q 91953 4 91348 5 42972 21828 5 TES660 3 T5590 0 701013 1 65579 0 829714 0 12092 21955 ESTs Weakly similar to M ALI 0 671476 0 21145 3 36957 1 13132 Input Data 1 Dataset Name 2 Type of Data 3 Model Number 4 Lead Columns before Data 5 Dataset Information 6 Column Name Row 7 Classifidcation Vector 8 Shape Vector 9 Pair Vector A Data Row Description To simplify the process of data importation GenePilot uses a template format This structured template uses keywords and tab delimiting for creating an intuitive template to provide GenePilot with the information necessary for the best results while analyzing your data In the description of the fields below required information is marked with lt required gt Each required row must be in the order as laid out in the template It is recommended that you use a spreadsheet to create this data then save it as tab delimited text A very important part of the input data is the Vectors Section In this section you can define Classification Vectors Shape Vectors and Pair Vectors These vectors can be used as supervising vectors in the Super
27. Dataset Template Replicate Column Vector 6 Row Type 6 Creating Dataset Templates 6 Select Data Chip Type 6 Data Adjustment Data Adjustment Options 15 Filtering Options 15 Linear Calibration 15 Mean Centering 15 Median Centering 15 View 13 Data Adjustment Settings 15 Dataset Archive Dataset 13 Close 13 Export Dataset 13 Filtering Options 15 Graph Panel 16 Import 13 Information Panel 16 Load Dataset Archive 13 Make Template 13 Missing Data Imputation 16 New 13 Open 13 Results Panel 16 Save 14 Select Current 14 Vew Info 15 View Heatmap 14 Dataset Display 22 Copy to Clipboard 23 Copy to Clipboard Interface 29 Copy to File 24 Copy to File Interface 29 Create Vector 24 Field Info Url Targets Interface 26 Gene Ontology Display Settings 24 Gene Ontology Statistics 24 Heatmap Panel 22 Help 24 Launch Info Page 24 Make Bitmap 23 Normalize Rows 25 Palette 31 Quit 24 Row Info Display 26 Row Information Page 32 Row Information Window 31 33 Search 24 30 Search Again 25 Select Heatmap 25 Url Lookup Editor 33 View Adjusted Data 25 View Filtered out Data 26 View Original Data 25 Dataset Info 16 E Enzymatic Function Creating Dataset Templates 7 Export Export Dataset 13 Export Dataset 13 Exporting Archive Dataset 13 F FDR Graph SAM 78 Field Info Url Targets Interface Dataset Display 26 GenePilot 14 92 GenePilot V 1 07b August 28 2003 Index Hierarchical Clustering 43 K Means Cluste
28. E cic bn o EIU SEE ein ve Eon Enc PER bonu E EFL H E ee repe E E 53 Windows Create Dataset p 56 Preferences Row Info Display oisicicccsassicectivecescccdececcesstecacecateticnssccdeescsveacsecseoseestied 57 Preferences Gene Ontology ssssssssssssiossassosisssssassssssssssosdossisissos sssnssossesossosissse sasss 58 Interface Copy to Clipboard essssssccecssssscceccssoocececssoocecessssocecssssscsecessoscesesssssse 60 Interface Copy gno P 60 Interlace SEAL T 61 Chapter 6 SOM eoc0c00000000000000000000000000000000000000000000 62 Run Settings mM Q 63 Results Parts Node Panel esessssooecsssosccecessooeecesssoooecsssssoccesssosececesssosssesssssseee 64 Results Parts Heatmap Panel seseesssooosessssocccesessooecesssococeessooeecessscsosesssssesseseo 65 Results Men Choit S cose dsctsccsccbcccensdestuccicssdosasecdevtcdesseddetestecseccestadtisuensadedissasecetics 67 Windows Create Datasets cccccssssxceississvavisssves cscecndsessenteus sbensaseesstuvessonssssesestusvessens 70 Preferences Row Info Display eesssecoecssssooceesssooccecessoocececssoooecessssoseesssosesecessssse 71 Preferences Gene Ontology sisissssssssiscsessssssscssesessosssusssdscsoscosasasssanscssssossss si eascs3s 72 Interface Copy to Clipboard ssessssccessssssocecessoocesesssoooecessssocecsssososecess
29. Edit gt This entry provides information to the import code to indicate where the Data Columns start Do Not Edit Input Information lt Optional Recommended gt This entry provides information about the dataset that is displayed with the Dataset Information This information is especially useful when several versions of the same Dataset are being used and specific entries are made to explain the differences The Information must be located in the second column with the first column starting with Information Input Column Names Required Column names define the names for each column that are displayed in the result windows It is very important to choose names that will make sense when viewing the results Each name should be placed above the corresponding column of data starting in the 5th column The first column must start with Column Names Input Vectors Replicates Vector Optional This entry ties the replicate columns together which represent the same experiment Starting with 0 zero assign the same number to each replicate for an experiment If there are three columns of data for each experiment then there should be three 0 s three 1 s three 2 s etc The following describes the entries needed Column 1 leave blank Column 2 Vector Type Must begin with Replicates Column 3 Vector Name Must be Replicates First Data Column to last Number representing which column gr
30. Gene Pilot v1 07b IS CenePiet 10b fe View umen Window Hep oe Coat C Camis Chip Typis GenePilot V1 07b August 28 2003 Table of Contents Chapter 1 Getting Started 1 PTAS CANT ARION mc HZ Windows Instructions bte 2 Mac OS Classic 8 1 or greater Instructions cccsssccccssessssrccsssssssssscssssseesees 2 Mac OS X Wide 2 Solaris iii reir rt T D 3 Linux Instr cliOllS 5vceieoiiepe t eiectus entero sai retro Dopo reb opa T sosb p CIPUE Keep E be R dieien in 3 HP UX Instructiolis ie te ene nee an es nen eee See TREASURE EE DES a RES eee 3 Generic Unix Instructions wcssicsecoedessiiccdceecicassestescideaanscdseexiviccstenedaecstsudewssecioseeenseins 3 All Other Platforms Instructions 142 eeeresieiesse secte ta ouo netus e Du S Da Ro eue pae PERO ex SES deb z a peres 4 jin me 5 Creating Dataset Templates 222 2 deor ci I Speo EEoEERE F v VER EcES YES PeGER ED RN PIE SPP S Ebx isise REP ue pOE 6 Preparing Pcr e 8 Chapter 2 Main Window 12 Menu Choices T caa si 13 Data Adjustment Settings ssessssccscssssscceceesoscceccssooeccesssocoecesssoosecssssscosessssocsessssosee 15 Filtering OPtiOnS sissssisissssssesiiseasisuostsusnssasestpnnosisssusonaoues sdr ciseu kasao va PERDERE
31. Info Display prerermmmmmmmm s Description Row infe Field Selection Paral Select mepo cha The Row Info Display Preferences Window is used to Tcv specify the Row Information fields that will be displayed select finr ntu ritus to the right of the Heatmap In addition to selecting the fields the field order can be specified along with the Lniena Symba character separating the contents of each field Fields AS UniGene Name DR are selected for inclusion by moving them from the left REDDAM column Available over to the right column Included Fepeesenkilios mRNA ACC The order of display is set by their row order with the Feepersentative Protein Ac first row being the first display field UaiDena Caster iD Select separator char l This selection sets the character that will separate the at l e information from each field Row Info Field Selection Panel Select Row Info Fields This section allows for selection of the specific fields that will be displayed in the row info and the order of these fields It has the following buttons gt gt This button moves the currently hilited field in the left column over to the right column lt lt This button moves the currently hilited field in the right column over to the left column up This button moves the currently hilited field in the right column up one row down This button moves the currently hilited field in the right column down one row Button Make
32. Information Fields that are 7 ioess Sebel chosen 7 LeeusLinkiD T Uskana Name Select File Path F gumman Forumen This selection is used to set the path to the output file Click onthe tananisiogrisnsiatoss Set Output Path to set the file Traditional copy and paste Rapessertattvo rRNA ace methods work in this field 9 pearen Prin AC sijana Counter it Copie Fea cancer Copy to File Interface 60 GenePilot V 1 07b August 28 2003 K Means Clustering Search Interface Select how much data to copy This section determines which rows will be selected When All Rows is selected then all of the rows in the current cluster are copied to the file or all clusters along with their rows are copied if no cluster is selected When Selected Rows is selected If rows are selected in the Heatmap only those rows will be included If a cluster is selected but no rows are selected all rows in that cluster will be included If no cluster is selected then all clusters along with their rows will be copied Select Row Information Fields to include This section allows the user to specify which rows they d like to include in the Copy to File Each Row Information Field that is checked will be included in the copy Button Copy to File This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy LTTEENMEERESS Interface Search f
33. Information Fields which the user is interested in Create Vector Action gt Create Vector This selection launches the Create Vector dialog box along with the mean vector of the currently selected rows Gene Ontology Display File gt Preferences gt Gene Ontology Display This selection launches the preferences window for Gene Ontologies Within this preference window the following can be set set number of columns set automatic preferences for selection of Gene Ontologies select specific Gene Ontologies to display 67 GenePilot V 1 07b August 28 2003 SOM Menu Choices Generate Gene Ontology Statistics Action gt Generate GO Statistics This selection launches an html page that contains the statistics for the Gene Ontologies for the rows in the following order of precedence If in Node 1 Selected Rows 2 All NodeRows If in All Node 1 All Rows in Selected Nodes 2 All Rows in all Nodes Launch Info Page Action gt Launch Info Page This selection launches an information page containing a matrix of the genes vs Gene Ontologies if available and a listing of all of the Row Information Fields along with links to websites which have further information Copy to Clip Selected Action gt Copy Sel to Clip This selection copies the currently selected Rows to the system Clipboard along with row information and column headings If no rows are selected but a node is selected then all of the rows in the current cluster are copied to th
34. Interface Selecting Visible Fields restricts the search to just the information that is visible as set in the Preferences gt Row Info Display Selecting All Fields causes the search to include all Row Info Fields whether visible or not Select Case Sensitive Checking this box will cause the search to be case sensitive Button Search This Button activates the search Button Cancel This button closes the interface without searching 30 GenePilot V 1 07b August 28 2003 Dataset Display Row Information Page Common Windows Row Information Window Description LI x The Row Information Window displays all of the Row Infe Orig Rew Num 1353 information that GenePilot knows about the lniana Sprick COKNDA current row of information This window is pree n Sepencdent k rn inia 24 jma pls inhibits CDU Borrich F uscbns Cy br Zezesdant ncs nies 1 iach ETE eta 7I launched by clicking on a row within the Row Info 1 1 5 b ined eromen adie hier nalr Gee bee A A ETTA section of a result screen Itis a single row kme perprarnerjmrtecelar mci EROR F Proisa ON 1 1 1 1 bell ore amegbsosica peecusdi Ko Posten hat Too version of the Info Page that contains information Deli pycha Bigong al props EIGHT SIPTORe oma 7 97 2808 about one or more rows of information a acute resumen nf cel priala bonaji al eroi pO OE PAP mes i i posl abon of CODE iehiga ai process Exe GP robe onm 97 23088 hashtable showing the
35. Norm This selection changes the heatmap to show each row normalized That means that the color corresponding to the highest value in the palette will be applied to the highest value in the row the color corresponding to the lowest value in the palette will be applied to the lowest value in the row and all other values will be scaled accordingly Show Rows Un Normalized Normalize gt NoNorm This selection displays the traditional heatmap display where color selections from the palette are determine from the highest and lowest value among the data not just in a row View Original Data Show gt Original Data This selection shows the original data that was imported into GenePilot View Adjusted Data Show gt Adjusted Data This selection shows the adjusted data if preprocessing has been done on the Dataset This means that rows that have been filtered out are not included missing data has been filled in through calculations and the Data has been adjusted 25 GenePilot V 1 07b August 28 2003 Dataset Display Row Info Display View Filtered Out Data Show gt Filtered Out Data This selection shows the Rows of data that have been filtered out during preprocessing Url Targets for Row Fields Interface File gt Preferences gt Field Info Urls This selection launches the preferences window for Field Info Target Url Window Selection Windows gt lt Window Name gt This selection brings the selected window up to the front Preferences Row
36. Preferences Select control for Gene Ontology Columns This selection sets the way that Gene Ontology Columns are selected with the following options Auto Selection Chooses most common Gene Ontologies among selected rows if avail then fills in remaining if necessary from most common among remaining rows Auto Set Chooses most common Gene Ontologies among displayed rows User Select Displays rows that the user has specifically selected This gets turned off when the user clicks on the Gene Ontology Names Select or View Gene Ontology Entries This section is for viewing or selecting specific Gene Ontologies by checking the checkbox either manually or using the Select Top button under the list List Show Choices This selection sets the Gene Ontologies that will be displayed in the list for selection It has the following choices Show All GO Displays all of the Gene Ontologies that are associated with the current Dataset Show only GO from Set Displays the Gene Ontologies that are associated with the currently displayed genes Show only GO from Selected Displays only the Gene Ontologies that are associated with the currently selected genes List Order Choices This selection sets the order that the Gene Ontologies are displayed in the list for selection It has the following choices Sort by name Sorts the Gene Ontologies by their name Sort by Set qty Sorts by the number of times that each Gene Ontology is associated to a
37. Row Info Display Preferences Window is used to specify the Row Information fields that will be Select Row nio Fiekis displayed to the right of the Heatmap In addition to selecting the fields the field order can be specified Leitung Symbol along with the character seperating the contents of each eee field Fields are selected for inclusion by moving them agn from the left column Available over to the right column Included The order of display is set by their Fepeezenzyme Proven Ar row order with the first row being the first display field 9e cetero Gane Orfclogs Annotate Reprene maha Acc Select separator char This selection sets the character that will separate the information from each field Row Info Field Selection Panel Select Row Info Fields This section allows for selection of the specific fields that will be displayed in the row info and the order of these fields It has the following buttons gt gt This button moves the currently hilited field in the left column over to the right column lt lt This button moves the currently hilited field in the right column over to the left column up This button moves the currently hilited field in the right column up one row down This button moves the currently hilited field in the right column down one row 57 GenePilot V 1 07b August 28 2003 K Means Clustering Gene Ontology Preferences Button Make Changes This button must be clicked in order for th
38. Row Information Page cccssssssccscsssssscccsssssssssccscsssssscssees 32 Common Interfaces Url Lookup Editor cssssccccssssssssccscssssssccccsssssssccsees 33 Chapter 4 Hierarchical Clustering 35 R n Settings e 36 R sulis Parts Left Paliel oce ee einccce ues sees feuis eue toa non DER tte Ee Rue Ee bun EP UR E eo eene Ea 37 Results Parts Editum T 39 Results Menu C IOIC S 2 2 enriicince sues ee Pinus cuore saca eue eub SES eo ee ee Pe eben E SUP EN Penn ERE e e Fes besE PUE 41 Int rface EI cU 43 Preferences Row Info Display 54 us eieiieeku eese epo a aco aos b S consu vi eb SE oe sera es ex E resa suo eee 44 Preferences Gene Onfol05By eite teinte ere o Ebene aae ea ees ae ee ruv CER e SES DE CF e aded 45 Interface Copy to Clipboard 2 siiiieeieeece tenure apos ert opos na toco eese v sa eo ee res pea eso ex eese sius 47 Interface Copy t We cec 47 Intertace cire M 48 Chapter 5 K Means Clustering 49 Run Settings Me PT P 50 Results Parts Graph and Button Panel e eee eee e eese e eee eere eee te 50 Results Parts Heatmap Panel eiie errorae eere FPE perro ec OF ore e ene E oC karen pee cnEvs 52 Results M nu C BOIC S 2 iniecit inen pou odd Se sen e
39. S teases 15 Data Adjustment Options essesssoseesssssccesessssccccessoococeessooeecssssocoecesssesocessosscsessssssse 15 Missing Data Imputation Options ssessssssoccssssooccecessosoessssssoocessssoosceessosossesssssose 16 BETETE Di KEEA E E E E E E 16 Interface Row Info DupOEL sssssssssssieisoscssisuidssossuscusstie osissip asassssstens drasiai roseacists 17 Interface Replicate Column Combine Panel esessssosssessssoocecessocoseessoososeessossee 18 Chapter 3 Dataset Display 21 Parts Heatmap Panel sisssisssississsctssiiusossssnsunsisotsuroniszssusdisuipuadsessadnrniosasuaoitiss inesatta 22 Dataset Display Menu Choices sssseoeesesssoccecsssoocoeccssooeecesosoosecessosooeeesssossseessssse 23 Preferences Row Info Display sessseccessssssececsssooececessooeecssosoooecessssooeessssocsecessssee 26 Preferences Gene Ontology sssssesssssocccessosococcsssooececessooeecessoooocessosscceesssoossecesssse 27 Interface Copy to Clipboard sssisssccessscsnsececscessvsnnctescescdeszeedecscatadtosncceevactaatenesinceces 29 Interface Copy to WMG scicsecesecasseceretcacicenceuccosecssancdetieedeancacceeetceaseacauccaeiecteintivessetces 29 Interface 2 eS SPO ee ene ene er 30 Common Windows Row Information Window 4 eee eere eene eene 31 Common Windows Palette icsese eee epe ae boa ne assu nn a Fa RUsEeabosUroE asas Pa aeuo aRa a ra auh 31 Common Page
40. Sun s Java web site or contact your OS manufacturer Generic Unix Instructions Instructions After downloading open a shell and cd to the directory where you downloaded the installer At the prompt type sh GenePilot_v1b bin Notes You need to install a Java 1 1 8 or later virtual machine You can download one from Sun s Java web site or contact your OS manufacturer 3 GenePilot V 1 07b August 28 2003 Getting Started Installation All Other Platforms Instructions Instruction Unix or Unix like operating systems For Java 2 after downloading type java jar GenePilot vlb jar If that does not work try java classpath path to classes zip GenePilot_v1b jar install If that does not work either on sh like shells try cd to directory where GenePilot_v1b jar is located CLASSPATH GenePilot v1b jar export CLASSPATH java install Or for csh like shells try cd to directory where GenePilot_v1b jar is located setenv CLASSPATH GenePilot_v1b jar java install Instructions for other platforms Be sure you have Java 1 1 8 or later installed You can download Java from Sun s site In aconsole window change to the directory where you downloaded GenePilot_v1b jar to before running the installer Your operating system may invoke Java in a different way To start the installer add GenePilot v1b jar to your CLASSPATH then start the main class of the installer named install 4 GenePilot V 1 07b August 28 2003 Getting Started Tutori
41. a Gara Drel lene Irr binis List Shoe Choices List Order Choices aa 5s Ler Shy Gara Dr co Hame Chester qe ieagrai lo glas marmsrass4 sigealtransducSen t 4 ekcer Space 12 eeeacediolar eatin rnt Geter Top Unsetertas See Changes Casco nene Gene Ontology Settings Panel This selection sets the Gene Ontology Categories to Display with the following options Biological Process Shows only Biological Process Cellular Component Shows only Cellular Component Biological Process amp Cellular Component Shows both Categories Molecular Function Shows only Molecular Function Biological Process amp Molecular Function Shows both Categories Cellular Component amp Molecular Function Shows both Categories AII Shows all three Categories Select control for Gene Ontology Columns This selection sets the way that Gene Ontology Columns are selected with the following options Auto Selection Chooses most common Gene Ontologies among selected rows if avail then fills in remaining if necessary from most common among remaining rows in the node Auto Node Chooses most common Gene Ontologies among the rows in the current node User Select Displays rows that the user has specifically selected This gets turned off when the user clicks on the Gene Ontology Names Select or View Gene Ontology Entries This section is for viewing or selecting specific Gene Ontologies by checking the checkbo
42. aa Ge Description Enter Search Sring This interface is used to set the search term and the settings for the search SEES eee The search can be restricted to just the visible Row Information or to all Selec Row Infarrmanion to Search Row Information It can also be set to be case sensitive The search Cow Finis Fam Fhe function remembers the last row that it searched in a cluster When a new cluster is selected that information is reset Select Case Senate yes Seach cance Enter Search Str ing l Search Interface The search string is entered into this field Traditional copy and paste methods work on this field Select Row Information to Search Selecting Visible Fields restricts the search to just the information that is visible as set in the Preferences gt Row Info Display Selecting All Fields causes the search to include all Row Info Fields whether visible or not Select Case Sensitive Checking this box will cause the search to be case sensitive Button Search This Button activates the search Button Cancel This button closes the interface without searching 61 GenePilot V 1 07b August 28 2003 SOM Description SOM is acommonly used unsupervised method for analyzing MicroArray Data Itis a top down Clustering method with a grid of nodes square or hexagonal which influence the vector shape of the adjacent nodes which are in their neighborhood The grid is initially seeded with
43. acting it from 1 in row clustering distance calculations If the absolute value is used then two vectors that are mirrors vertically of each other will cluster close to each other If the absolute value isn t used then two vectors that are mirrors of each other will not be clustered together 36 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Results Left Panel Group Anti correlated Cols with Correlated Cols Checkbox This setting determines whether the value Pearson s Correlation will be made an absolute value before subtracting it from 1 in col clustering distance calculations If the absolute value is used then two vectors that are mirrors vertically of each other will cluster close to each other If the absolute value isn t used then two vectors that are mirrors of each other will not be clustered together Memory Model Small Faster Large Larger Clusters This setting determines how many stored distances are used for row clustering A simple model of Hierarchical clustering stores every distance between every row What this means is that if there are n rows then the size of memory required to run will be n x n 1 x 4 where 4 is the number of bytes necessary to hold the information This means that for a 10k row dataset 400megs of ram will be used just to hold the distance calculations The alternative is to calculate the distances every time leading to prohibitive run times The solution that GenePilot
44. als Tutorials Sample Data We highly recommend that you go through the tutorials especially the Sample Data tutorial Within this tutorial you will be walked through the whole process of bringing a Dataset into GenePilot and stepping through most of the features that GenePilot has to offer You can access this tutorial with Help gt Tutorials gt Sample Data once you have launched GenePilot We estimate that the average user can get through the comprehensive tutorial in about two hours unless they get side tracked by the very interesting and actual data that is used in the Tutorial This sample data is the NCI T Matrix1375 data which contains gene expression results from various kinds of cancer Your Data When you have completed the Sample Data tutorial or choose to skip the tutorial and are ready to import your own data we highly recommend that you use this tutorial to walk you through the process of importing your own data for the very first time 5 GenePilot V 1 07b August 28 2003 Getting Started Creating Dataset Templates FE Make Dabaset Template Creating Dataset Templates Make Dataset Template Window Seieci Desi Fie Pat Description Select Date Chip Type Other 9 DHA C ay The very first step which needs to be taken in order to analyze data in GenePilot is to export a template which is specific to the Dataset By exporting a Gal Celemes ah appie to Ay Data inchs Replicate Column vector O template i
45. an be excluded from a new Dataset Quit File gt Quit This selection closes the Result Window Save Results File gt Save Results This selection is used to save the current result This will save the results of an Analytic run so that the results can be viewed immediately Once an analytic result is saved for a Dataset a button will be added to the Dataset Information screen to quickly view the saved result Search Action gt Search This selection launches the search interface which allows the user to search the rows for a String See Search Interface for more information on the Search Interface For Hierarchical Clustering the search will search the currently selected cluster from left Panel first it will then search beyond that and start at the beginning when it reaches the end of the Dataset Search Again Action gt Search Again This selection searches for the next case of the search string Select Classification Vector If Avail Classes gt Class Vector Name If there is one or more Classification Vectors then one of those vectors can be selected for class indication of columns in either the Column Dendigram if column clustering was selected or the Class Indicator in the Right Panel Select Heatmap Palette Red Green Palette gt Red Green This selection selects the traditional colors of Red and Green for the heatmap Red is positive or Correlated and Green is negative or Anti Correlated Select Heatmap Palette
46. at each Dataset name must be unique Set Description for Combined Dataset This field is for setting the description of the combined Dataset By default the description of the current dataset is placed in this field We recommend that you add a description of what selections you used to produce the combined dataset Select Type of Combine These radio buttons offer the selection of the type of method that will be used to combine the values in the replicate columns If there is only one value then that value is used If there are two values then the Average of those two values are used If there are three or more values then the choices are Median Value The median value is used Mean Value The Mean or Average value is used Weighted Mean Value The weighted mean value where the weight is equal to 1 variance Choose what to exclude Currently there is one choice of what to exclude Exclude Selected Rows This allows for selecting the worst rows in the dataset to exclude Choose Row Order There are currently two ways to sort the statistics information in the Column and Row Statistics Display They are 95th Percentile Quantity The row order is determined by the count of cels in Row where the SD Mean of the Combined Data shows a value in the top 5 percent as the primary count and the average value for SD Mean With a maximum cut off value as a secondary sort Average StandDev over Mean The row order is determined by the average val
47. ata to copy mE bene This section determines which rows will be selected When All Rows is 7 isst selected then all of the rows in the current cluster are copied to the Unies Hame clipboard or all clusters along with their rows are copied ifnoclusteris F SussmaryFenesen selected When Selected Rows is selected If rows are selected in the T Gime etstogyAnnotamans Heatmap only those rows will be included Ifa cluster is selected but no P emseees ma Ace rows are selected all rows in that cluster will be included If noclusteris P eee ree selected then all clusters along with their rows will be copied E Cem cenbeard Cancel Select Row Information Fields to include Copy to Clipboard Interface This section allows the user to specify which rows they d like to include in the Copy to Clipboard Each Row Information Field that is checked will be included in the copy Button Copy to Clipboard This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy E Copy Lo Fide infornnakien Copy to File intertace Sting File Pathe D Pesiact Tanapieterine bp bd Bud tupai Path Interface Copy to File Description TREE EE This Interface allows the user to select specify a File Path in which to write out information contained in this result This information will amp csi include the rows specified and the Row
48. ays the traditional heatmap display where color selections from the palette are determine from the highest and lowest value among the data not just in a row Url Targets for Row Fields Interface File gt Preferences gt Field Info Urls This selection launches the preferences window for Field Info Target Url Windows Create Dataset E veote Datt fromm CET Habri 1375 out STE Create Sub Dataset Interface Description Set Columns to inckude Defaui ME Select Columns This Interface is used to create anew Dataset by using seteswDataset info one or more clusters for defining either the rows in the Generated ross the NCI T Matea 1375 new dataset or the rows to be excluded in the new Dataset In the current cluster the selected rows can be used to further refine the selection Set New Dataset Name This text field is the name that the new Dataset will rens receive Itis seeded with the result Dataset Name mir along with KM to indicate that it was created using Chester the results from a K Means Clustering result screen Choe 4 Chenier 5 Cheer B Create Creede Caachi Me That name can bet set to anything as long as the name is not already in the system Create Sub Dataset Interface Select Columns to Include Default All The button Select Columns launches a window that allows for selection of the columns to be included in the new Dataset If no column selection is made then all columns will be us
49. beginning cluster Search Again Action gt Search Again This selection searches for the next case of the search string using the settings from the previous search 68 GenePilot V 1 07b August 28 2003 SOM Menu Choices Select Classification Vector If Avail Classes gt Class Vector Name If there is one or more Classification Vectors then one of those vectors can be selected for class indication of columns in either the Column Dendigram if column clustering was selected or the Class Indicator in the Right Panel Select Heatmap Palette Red Green Palette gt Red Green This selection selects the traditional colors of Red and Green for the heatmap Red is positive or Correlated and Green is negative or Anti Correlated Select Heatmap Palette Yellow Blue Palete gt Yellow Blue Default This selection selects the traditional colors of Yellow and Blue for the heatmap Yellow is positive or Correlated and Blue is negative or Anti Correlated Select Heatmap Palette Gray Scale Palette gt Gray Scale This selection selects shades of gray for the heatmap Light Gray is positive or Correlated and Dark Gray is negative or Anti Correlated Show Palette Palette gt Show Palette This selection Launches the Palette Window which shows the color palette used by the heatmap Show Rows Normalized Normalize gt Norm This selection changes the heatmap to show each row normalized That means that the color corresponding to the highe
50. ce date te Coy a Beieted Rows OC Ane Scho Fire befor ratte Fick s inc hee Chana iD Unders Symbol LecusLink iD uera Hame 4 tummar Fonckon Omne Criit Aroari O Ripiririse mrad ace Rapneentates Protein Acc Unitas Chuster Di Certo Capboard cancei Copy to Clipboard Interface This section allows the user to specify which rows they d like to include in the Copy to Clipboard Each Row Information Field that is checked will be included in the copy Button Copy to Clipboard This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy Interface Copy to File Description This Interface allows the user to select specify a File Path in which to write out information contained in this result This information will include the rows specified and the Row Information Fields that are chosen Select File Path This selection is used to set the path to the output file Click on the Set Output Path to set the file Traditional copy and paste methods work in this field 47 B Copy ta Pile inlerine xj Copy to File intertace Soto File Pathe Dwesiechi oinpe bp bd But Dufpet Path Fek how much dara ta copy OF Gebiede C MP Reet ihi Pitre iniiai Fitek Da ipeckede 7 cione D T Uaiena gmba F LeeusLink iD ueiness Name Hussmarg Fenian dans Ontolozr Anciens Raepaxanmueme mita ace Fesges
51. ch case all the rows in the current delta will be included 88 GenePilot V 1 07b August 28 2003 SAM Search Interface Select Row Information Fields to include This section allows the user to specify which rows they d like to include in the Copy to File Each Row Information Field that is checked will be included in the copy Button Copy to File This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy Interface Search EE x Description Search Interface This interface is used to set the search term and the settings for the search Enter Search Sring The search can be restricted to just the visible Row Information or to all Row Information It can also be set to be case sensitive The search Shit Raw infitrarion to Search function remembers the last row that it searched in a set When a new set is Coa Fwd T Anois selected that information is reset Select Case Senate Yes Enter Search String Search Cancel The search string is entered into this field Traditional copy and paste Search Interface methods work on this field Select Row Information to Search Selecting Visible Fields restricts the search to just the information that is visible as set in the Preferences gt Row Info Display Selecting All Fields causes the search to include all Row Info Fields whether visible or not Select Case Sensitive Checking this box will cause
52. ckwise by 90 degrees above each column in the Heatmap Gene Ontology Names Middle Right If Gene Ontology Information The Gene Ontology Names is a variable column display that displays the Gene Ontology Names that are currently chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set If specific Gene Ontologies are selected by the user the settings can be easily changed back to automatic selection by clicking on this Gene Ontology Names display Gene Ontology Indication Bottom Middle The Gene Ontology Indication indicates the Gene Ontologies that are associated with each row The Gene Ontologies are chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set Correlation and FDR Column Bottom Middle This column indicates whether a row is correlated red or anti correlated green with the input vector It also indicates the FDR value percentage for this row Row Information Bottom Right Row information contains the row name and row information to the right of each row in the heatmap Class Information Top Right If Class Vector If there is Classification Vector s there will be Class Information which defines the color coding for the Class Indication row Actions
53. click GenePilot_v1b exe Notes Requires Mac OS X 10 0 or later The compressed installer should be recognized by Stuffit Expander and should automatically be expanded after downloading If it is not expanded you can expand it manually using StuffIt Expander 6 0 or later If you have any problems launching the installer once it has been expanded make sure that the compressed installer was expanded using Stuffit Expander If you continue to have problems please contact technical support 2 GenePilot V 1 07b August 28 2003 Getting Started Installation Solaris Instructions Instructions After downloading open a shell and ed to the directory where you downloaded the installer At the prompt type sh GenePilot_v1b bin Notes You need to install a Java 1 1 8 or later virtual machine You can download one from Sun s Java web site or contact your OS manufacturer Linux Instructions Instructions After downloading open a shell and cd to the directory where you downloaded the installer At the prompt type sh GenePilot_v1b bin Notes You need to install a Java 1 1 8 or later virtual machine You can download one from Sun s Java web site or contact your OS manufacturer HP UX Instructions Instructions After downloading open a shell and cd to the directory where you downloaded the installer At the prompt type sh GenePilot_v1b bin Notes You need to install a Java 1 1 8 or later virtual machine You can download one from
54. clude is selected only the rows designated will be used in the new Dataset When Exclude is selected the rows designated will be subtracted from the rows that made it through the filtering process if any to create a new Dataset Use Current Selected Rows and Use Current Cluster Radio Buttons These radio selections only show up if rows are selected in the right panel otherwise the entire cluster selected in the Left Panel will be used If Use Current Selected Rows is selected then the rows selected in the Right Panel Heatmap will be used If Use Current Cluster is selected then the rows contained in the currently selected cluster will be used Button Create Dataset This button creates the new Dataset Button Cancel This button closes the interface window without any further action Preferences Row Info Display _ EEE Description eee eee re s Select saqusraior chai The Row Info Display Preferences Window is used tO eem specify the Row Information fields that will be Select Row info Fields displayed to the right of the Heatmap In addition to selecting the fields the field order can be specified Lining Genter along with the character seperating the contents of each SO E field Fields are selected for inclusion by moving them Darm nkblopr ansia from the left column Available over to the right Fepeesentiive mANA Acc column Included The order of display is set by their Fiepeesarnfative P
55. cting the Row Information Fields which the user is interested in Copy to File Action gt Copy to File This selection launches an interface for copying all or selected rows to a file This interface also allows for selecting the Row Information Fields which the user is interested in Create Vector Action gt Create Vector This selection launches the Create Vector dialog box along with the mean vector of the currently selected rows Gene Ontology Display File gt Preferences gt Gene Ontology Display This selection launches the preferences window for Gene Ontologies Within this preference window the following can be set set number of columns set automatic preferences for selection of Gene Ontologies select specific Gene Ontologies to display Generate Gene Ontology Statistics Action gt Generate GO Statistics This selection launches an html page that contains the statistics for the Gene Ontologies for the rows in the following order of precedence If in Cluster 1 Selected Rows 2 All Cluster Rows If in All Clusters 1 All Rows in Selected Clusters 2 All Rows in all Clusters Launch Info Page Action gt Launch Info Page This selection launches an information page containing a matrix of the genes vs Gene Ontologies if available and a listing of all of the Row Information Fields along with links to websites which have further information Make Dataset Action gt Make Sub Dataset This selection launches and interface that let s the
56. d rows Gene Ontology Display File gt Preferences gt Gene Ontology Display This selection launches the preferences window for Gene Ontologies Within this preference window the following can be set set number of columns set automatic preferences for selection of Gene Ontologies select specific Gene Ontologies to display Generate Gene Ontology Statistics Action gt Generate GO Statistics This selection launches an html page that contains the statistics for the Gene Ontologies for the rows in the following order of precedence 1 Selectd rows 2 All rows being displayed Help Help gt Help This selection shows the Help for the Dataset Display Help PDF Help gt Help PDF This selection launches an html browser with this User manual Launch Info Page Action gt Launch Info Page This selection launches an information page containing a matrix of the genes vs Gene Ontologies if available and a listing of all of the Row Information Fields along with links to websites which have further information Make Dataset Action gt Make Sub Dataset Not currently implemented Quit File gt Quit This selection closes the Result Window Row Info Display File gt Preferences gt Row Info Display This selection launches the preferences window for Row Information This preferences window is used to define the Row Information that is displayed to the right of the heatmap Search Action gt Search This selection launches the search interface which
57. d to indicate the class of each column as defined by the Class Information block in the Top Right corner 52 GenePilot V 1 07b August 28 2003 K Means Clustering Menu Choices Column Names Upper Left The Column Information contains the column names rotated counter clockwise by 90 degrees above each column in the Heatmap Gene Ontology Names Middle Right If Gene Ontology Information The Gene Ontology Names is a variable column display that displays the Gene Ontology Names that are currently chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set If specific Gene Ontologies are selected by the user the settings can be easily changed back to automatic selection by clicking on this Gene Ontology Names display Gene Ontology Indication Bottom Middle The Gene Ontology Indication indicates the Gene Ontologies that are associated with each row The Gene Ontologies are chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set Row Information Bottom Right Row information contains the row name and row information to the right of each row in the heatmap Class Information Top Right If Class Vector If there is Classification Vector s there will be Class Information w
58. down to the selected row This can be used to select rows in a group that is larger than those seen on the screen 3 When user selected gene ontologies are displayed the Gene Ontology displays can be reverted back to automatic mode by clicking on the Gene Ontology Names 40 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Results Menu Choices Results Menu Choices Bitmap from Selected Action gt Save Sel to Bitmap This selection creates a gif bitmap containing all of the information in the right Panel If no rows are selected in the Left Panel then it will not produce a Bitmap If rows are selected in the Right Panel then those rows will be included If rows are selected in the Left Panel but none are selected in the Right Panel then all rows in the Right Panel will be included in the Bitmap Bitmap from All Action gt Save All to Bitmap This selection creates a gif bitmap containing all of the information in the Left Panel Copy to Clip Action gt Copy to Clip This selection launches an interface for copying all or selected rows to the clipboard This interface also allows for selecting the Row Information Fields which the user is interested in Copy to File Action gt Copy to File This selection launches an interface for copying all or selected rows to a file This interface also allows for selecting the Row Information Fields which the user is interested in Create Vector Action gt Create Vector This selection launc
59. e NC T a 1 TS a Sat Vetter Lc brain crc erfuhr Sitiari isch 9 ee C Foppen oo Full Cancer hrpe Meera Lusg Cancer CNG Colin Creste Osea Caec vem Create Sub Dataset Interface The button Select Columns launches a window that allows for selection of the columns to be included in the new Dataset Ifno column selection is made then all columns will be used Select New Dataset Info This text field is the Dataset information field It is seeded from the result Dataset Information Additional information should be added here to provide a pedigree for the new Dataset Select Whether to Include or Exclude Selection When Include is selected only the rows designated will be used in the new Dataset When Exclude is selected the rows designated will be subtracted from the rows that made it through the filtering process if any to create a new Dataset Select Genes by FDR Checkbox and FDR value When checked the row FDR s will be used to select rows from all of the runs selected no selection necessary if only one run The FDR value sets the FDR to be used to determine rows selected Select Check Boxes These check boxes will only be available if the was more than one run i e The vector was a classification vector and the option to Run each classification against all others was selected These check boxes give the option to select each run to be used for defining the rows to be included or excluded 84 Ge
60. e changes to be made Button Cancel This button cancels any changes that were made and closes the window Preferences Gene Ontology SEE teere tobe Seti 8 09 Description pian brett ales agat This interface is used to set the Gene Ontology VULT os LE preferences for this screen The choices include H5 zi automatic selection of the most common Gene Seice G eiia C uktis Uer ieiki Ontology categories based upon either the currently Tadici o View Gana Onicloqe Dreit List Shoe Chokes List Onder Chas Soa ee Ler S selected rows or for all rows in the current cluster If the selected rows have preference and there aren t Gane Oniciogy Name Chester cho enough categories to fill the number of columns then AT etegent te plasma mamerase d the most common categories across all rows in the signal trasssucten 4 T iniraceliolar S paci 12 cluster are used to fill in the categories Specific Gene Ontology categories can also be specified this is aided by the List Show Choices and List Order Choices for quickly finding specific Gene Ontologies Select Number of Gene Ontology Columns to _Seiect Top unsetectan show Seer Changes Cancer Hip This selection sets the number of columns that will be Gene Ontology Settings Panel displayed Select GO Types in Display This selection sets the Gene Ontology Categories to Display with the following options Biological Process Shows only Biological Process Cellular
61. e clipboard If no nodes are selected then the node Vector will be copied to the clipboard Copy to Clip All Action gt Copy All to Clip This selection copies all Rows to the System Clipboard sorted by Nodes Make Dataset Action gt Make Sub Dataset This selection launches and interface that let s the user define criteria for creating anew Dataset from rows of the current Dataset For SOM one or more nodes can be selected with their rows to be used as the rows for the new Dataset or to be excluded from the new Dataset Note Rows that have been filtered out will be excluded from any new Dataset created this way Quit File gt Quit This selection closes the Result Window Save Results File gt Save Results This selection is used to save the current result This will save the results of an Analytic run so that the results can be viewed immediately Once an analytic result is saved for a Dataset a button will be added to the Dataset Information screen to quickly view the saved result Search Action gt Search This selection launches the search interface which allows the user to search the rows for a String with added options of searching visible Row Info fields or all Row Info Fields and case sensitive or not See Search Interface for more information on the Search Interface For SOM the search will search the currently selected node first it will then continue the search through the remaining nodes then start over at the
62. e default settings will be more than adequate Col Bimini Weim oop Ani Geminid ices win ComialerRDwr 7 Memor Modes mal Farin Lange Lupar Clusters ima Fan Reset View Saved Aua Linkage Measure This setting determines which part of a cluster is used to determine the distance from another cluster or row The choices are 1 Average The average vector for the cluster is calculated then used for calculating distances 2 Single The closest row vector ina cluster to another row vector or cluster is used for calculating distances Row Similarity Metric This setting determines how Pearson s correlation will be applied to the row clustering There are two choices 1 Correlation centered The row is mean centered before calculating 2 Correlation uncentered The row is not centered before calculating Cluster by Column Checkbox This Checkbox determines whether the columns of this dataset will be clustered If the box is checked the columns will be clustered Col Similarity Metric This setting determines how Pearson s correlation will be applied to the column clustering There are two choices 1 Correlation centered The row is mean centered before calculating 2 Correlation uncentered The row is not centered before calculating Group Anti correlated Rows with Correlated Rows Checkbox This setting determines whether the value Pearson s Correlation will be made an absolute value before subtr
63. e lowest value in the palette will be applied to the lowest value in the row and all other values will be scaled accordingly Show Rows Un Normalized Normalize gt NoNorm This selection displays the traditional heatmap display where color selections from the palette are determine from the highest and lowest value among the data not just in a row Url Targets for Row Fields Interface File gt Preferences gt Field Info Urls This selection launches the preferences window for Field Info Target Url 83 GenePilot V 1 07b August 28 2003 SAM Create Dataset Windows Create Dataset Description This Interface is used to create a new Dataset by using one or more nodes for defining either the rows in the new dataset or the rows to be excluded in the new Dataset In the current node the selected rows can be used to further refine the selection Select New Dataset Name This text field is the name that the new Dataset will receive Itis seeded with the result Dataset Name along with SAM to indicate that it was created using the results from a SAM result screen That name can bet set to anything as long as the name is not already in the system Select Columns to Include Default All FE Create Datel from SEE Patri 17S oul of SAM Create Sub Datasst Interface Sot ben Data Nama f 0C T Mates 1375 EAM Set Columas to include Defaui AN Gelert Coluesns Set Pier Co eset info Ceeree rated Brees m
64. e vectors can be selected for class indication of columns in either the Column Dendigram if column clustering was selected or the Class Indicator in the Right Panel Select Heatmap Palette Red Green Palette gt Red Green This selection selects the traditional colors of Red and Green for the heatmap Red is positive or Correlated and Green is negative or Anti Correlated Select Heatmap Palette Yellow Blue Palete gt Yellow Blue Default This selection selects the traditional colors of Yellow and Blue for the heatmap Yellow is positive or Correlated and Blue is negative or Anti Correlated Select Heatmap Palette Gray Scale Palette gt Gray Scale This selection selects shades of gray for the heatmap Light Gray is positive or Correlated and Dark Gray is negative or Anti Correlated Show Palette Palette gt Show Palette This selection Launches the Palette Window which shows the color palette used by the heatmap Show Rows Normalized Normalize gt Norm This selection changes the heatmap to show each row normalized That means that the color corresponding to the highest value in the palette will be applied to the highest value in the row the color corresponding to the lowest value in the palette will be applied to the lowest value in the row and all other values will be scaled accordingly 55 GenePilot V 1 07b August 28 2003 K Means Clustering Create Dataset Show Rows Un Normalized Normalize gt NoNorm This selection displ
65. eating Dataset Templates 6 S SAM 76 Bitmap 81 Copy to Clipboard 81 Copy to Clipboard Interface 88 Copy to File 81 Copy to File Interface 88 Create Dataset 84 Create Vector 81 Display All Data 81 Display Anti Correlated Data Only 82 Display Correlated Data Only 81 FDR Graph 78 Field Info Url Targets Interface 83 Gene Ontology 80 Gene Ontology Display Settings 81 Gene Ontology Settings 86 Gene Ontology Statistics 81 Heatmap Panel 79 Launch Info Page 82 Make Dataset 82 Normalize Rows 83 Palette 31 Quit 82 Row Info Display 85 Row Information Page 32 Row Information Window 31 33 Run 14 Run Settings 77 Save Results 82 Score Graph 78 Search 82 89 Select Palette 83 Save Results 95 GenePilot V 1 07b August 28 2003 Index SAM 82 Score Graph SAM 78 Search Dataset Display 30 Hierarchical Clustering 42 48 K Means Clustering 55 61 SAM 82 89 SOM 68 75 Search Again K Means Clustering 55 Select Palette SAM 83 SOM 69 Self Organizing Map See SOM 62 Self Organizing Maps Run 14 Settings Save 14 Shape Vector Creating Dataset Templates 7 Show Palette Hierarchical Clustering 43 K Means Clustering 55 SOM 69 Significance of MicroArrays See SAM 76 SOM 62 Bitmap 67 Copy to Clip 68 Copy to Clipboard 67 Copy to Clipboard Interface 74 Copy to File 67 Copy to File Interface 74 Create Dataset 70 Create Vector 67 Field Info Url Targets Interface 69 Gene Ontology Display Settings 67 Gene Ontology Settings 72 Gene O
66. ed Set New Dataset Info This text field is the Dataset information field It is seeded from the result Dataset Information Additional information should be added here to provide a pedigree for the new Dataset Set Whether to Include or Exclude Selections When Include is selected only the rows designated will be used in the new Dataset When Exclude is selected the rows designated will be subtracted from the rows that made it through the filtering process if any to create a new Dataset Select Check Boxes These check boxes give the option to select each cluster to be used for defining the rows to be included or excluded 56 GenePilot V 1 07b August 28 2003 K Means Clustering Row Info Display Settings Use Selected Check Box This check box is only available for the current cluster When checked only the selected rows will be used It is only shown when rows are selected in the heatmap Button Select All This button checks all of the Select Check Boxes making it more convenient to select most of the clusters Button Clear All This button clears all of the Select Check Boxes making it more convenient to turn off selection of most or all of the clusters Button Create Dataset This button creates the Dataset once all of the settings are made Button Cancel This button closes this interface without creating the new Dataset Preferences Row Info Display perma Description Rew Infe Field Selection Panal The
67. either random values or random rows Then successive rows are randomly selected and placed into the node to which their vector is closest Upon the placement of the row vector into the node the node vector is recalculated based upon the relationship of it s vector to the row vector Then the adjacent node vectors are also recalculated out to the extent of the current neighborhood size These neighborhood nodes are influenced to a lesser degree than the central node based upon their distance from the central node and the neighborhood type Aneighborhood is a decreasing with time sphere of influence that one node has on it s neighbors when each new row is placed within This process is then repeated for the number of iterations that are specified with the neighborhood decreasing in size throughout the process until the final iterations when only the central node is influenced In the result screen the nodes are displayed in their grid in the top pane Each node displays a small graph in the middle and a bar along the left side that indicates the number of rows that are represented by that Node The heatmap representing the vectors for these nodes are displayed in the lower panel until a node is select Upon selection of a node the heatmap and related information will be displayed so that the member rows and information can be examined For more information on SOM read more about it in Cluster Analysis for Large Scale Gene Expression
68. elect Valid Rarer info Files T cima 60 GenBank Accession E heii Name er IF LacusLinkiD Chromosome Lecaten ena Ai Lisi Name Summam Femin Gane Ontology Annotations Papubentve MANA Ace Pappe Promin AE Tiepa Winder Url Lookup Editor This Button saves the Currently selected Lookup as the Lookup for the current Row Info Field Button Reset saved Lookup Choice This Button restores the currently saved Lookup for the current Row Info Filed Select Lookup to Edit or Create New This selection is for selecting a Lookup to edit or choosing to create a new Lookup Name This selection displays the current name for a Lookup To update a name for an existing Lookup change the name in this field then click on the Update Cur Lookup button When creating a new Lookup the name of that Lookup will be entered here URL This selection displays the current Url for a Lookup To update a Url for an existing Lookup change the Url in this field then click on the Update Cur Lookup button When creating a new Lookup the Url will be entered here 33 GenePilot V 1 07b August 28 2003 Dataset Display Url Loolup Editor Select Valid Row Info Fields This section with it s check boxes sets the Row Info Fields which can use this Lookup Button Save Cur Lookup This button saves the new Lookup Button Update Cur Lookup This button updates the current Lookup Button Reset This button r
69. en Normalize is selected then the value range for each row is defined by the min and max values in that row with the mean value being the medium value Column Dendigram Top Column Clustering selected If Column clustering has been selected there will be a dendigram at the top If there is a Category Vector for this dataset the top dendigram will be color coded by class The column dendigram displays the cluster tree of the columns Similar columns are clustered together with either another column or a cluster depending on which is closer Distances can be roughly determined by the height of the node that binds the two entities columns or clusters together Row Dendigram Left To the left of the heatmap is the row dendigram The Row Dendigram displays the cluster tree of the rows Similar rows are clustered together with either another row or a cluster depending on which is closer Distances can be roughly determined by the distance of the node that binds the two entities row or cluster from the heatmap on the right Actions 1 Clicking ona node point of a cluster will select the cluster represented by that node The selected rows will be displayed in the right panel 2 Clicking on the heatmap and dragging the mouse while keeping the left mouse button depressed will select those rows Note that more rows than originally chosen will usually be selected as the program will look for a common node to the selected rows then select a
70. er the legend for the Class Indication will define the colors for each class when Classification Vector s are available When no node is selected this Panel will contain information about the node vector of each node When a node is selected then this panel will contain information about each member row for that node sorted in the order of the closest correlated for to the node vector to the furthest 65 GenePilot V 1 07b August 28 2003 SOM Heatmap Panel Heatmap Bottom Left The heatmap contains rectangles color coded in the Palette colors to represent the value of each cel juncture of 1 row and column By default these colors are Red highest value and Green lowest value When No Normalize is selected the value range is defined by the min and max values in the entire Dataset Rows remaining after filtering with zero being the medium value When Normalize is selected then the value range for each row is defined by the min and max values in that row with the mean value being the medium value Class Indication Above Average Heatmap If there is Classification Vector s there will be Class Indicators above the Heatmap This is a row of rectangles which are color coded to indicate the class of each column as defined by the Class Information block in the Top Right corner Column Names Upper Left The Column Information contains the column names rotated counter clockwise by 90 degrees above each column in the Heatmap
71. er to specify which rows they d like to include in Copy to Clipboard Interface the Copy to Clipboard Each Row Information Field that is checked will be included in the copy Button Copy to Clipboard This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy E Copy lo File inflates Interface Copy to File Copy to File interface Description Select Fie Falli This Interface allows the user to select specify a File Path in which CENCE Toe SeeC Ee to write out information contained in this result This information will 9997 Mae mach datata copy include the rows specified and the Row Information Fields that are 66 Gemini CA Ree chosen Geko Fra ior anon Fields na ichidh 7 cione ID Select File Path Usitoe gabai This selection is used to set the path to the output file Clickonthe IF Letwstna iw Set Output Path to set the file Traditional copy and paste T Daija Name methods work in this field 7 Sussmary Forutien Gans Orfcdogy ansians Select how much data to copy O Fapema mRNA Ace This section determines which rows will be selected When All 7 Eegen Prosan fec Rows is selected then all of the rows in the current delta range are ete Sse copied to the file When Selected Rows is selected then only the CoprioFea Cancel selected rows will be included unless there are no selected rows in Copy to File Interface whi
72. ers displayed When All Clusters is selected the graph will contain different colored lines representing the average vector of each cluster The color of each line corresponds to the color on the cluster buttons on the right 50 GenePilot V 1 07b August 28 2003 K Means Clustering Graph and Button Panel Graph Cluster n Value Plot zE Columns K Means Graph Cluster view When a cluster is selected in the button panel to the right of the graph the graph will contain a set of gray lines representing the vectors of each row in that cluster On top of all those lines will be a line representing the average vector of that cluster in the color that represents that cluster Button Panel To the right of the Graph is the Button Panel This panel will contain a button at the top named All Clusters then buttons below it with the label of Cluster n where nis to the number of clusters emmy ETE Actions Chet 1 Clicking on the All Clusters button in the Button Panel will display the m average vector for each clusters in the graph and will display the heatmap K Means Button representing the average vector in the heatmap panel below m a 2 Clicking ona cluster button in the Button Panel will display the vectors for all of the rows in a cluster along with the average vector for the cluster in the graph It will also result in the heatmap for the cluster rows to be displayed
73. es from the current cluster Show only GO from Selected Displays only the Gene Ontologies that are associated with the currently selected genes List Order Choices This selection sets the order that the Gene Ontologies are displayed in the list for selection It has the following choices Sort by name Sorts the Gene Ontologies by their name Sort by Cluster qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently cluster Sort by Selected qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently selected genes Button Select Top This button selects the Gene Ontologies that are at the top of the list in the quantity specified Button Unselect All This button unselects all of the currently selected Gene Ontologies Button Save Changes This button sets the currently selected settings and closes the window Button Cancel This button closes the window without setting any of the changes made 59 GenePilot V 1 07b August 28 2003 K Means Clustering Copy to Clipboard File Interface Copy to Clipboard Description This Interface allows the user to select which Row Information Fields to include in the Copy to Clipboard and to specify the rows that they want Cepyte Clipboard Intertace Geeni Perv reac date Se Coy 7 Haier Rows C ARROwE included in the selection usciti Paver inferens Fc e ic ade Cine iD Select how much d
74. esets the fields back to their saved settings for an existing Lookup and clears the fields for a new Lookup 34 GenePilot V 1 07b August 28 2003 Chapter 4 Hierarchical Clustering Description Hierarchical Clustering is one of the most commonly used unsupervised methods for analyzing MicroArray Data It is a bottom up Clustering method that starts at individual rows clustering rows clusters together until all of the rows and clusters are represented by a single cluster The columns can also be clustered in an identical manner This method provides a very good first look at the Dataset Patterns can be very easily spotted in the heatmap with the data clustered this way Utilizing the color coded column dendigram the quality of the samples can quickly be discerned by how well classes group together For more information on Hierarchical Clustering read more about it in Cluster Analysis and Display of Genome Wide Expression Patterns Reference 3 MB Eisen et al 35 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Run Settings Run Settings Linkage bisanun Row Suma Mab Description Chester byCoumne 7 The Run Settings provide a means to alter the way that Hierarchical Clustering analyzes the data It is recommended that the default settings be used prior to gaining more in depth knowledge on the ramifications of each setting Inthe Step Ae censeo con em Conmsimi Cos _ vast majority of cases th
75. ew gt Datset Info This selection is used to view the information that is displayed when a Dataset is opened or imported Data Adjustment Settings Filtering Options Percent Present gt n cDNA or Other This option filters out rows of data with less than n of present not missing values Less than n Negative Values lt p Affymetrix This option filters out rows that have at least n values less than p Standard Deviation Row Vector gt n All This option filters out rows of data that have a standard deviation of less than n At least n Observations abs Val gt p All This option filters out rows that have less than n values which have an absolute value greater than p Max Val MinVal gt n All This option filters out rows whose maximum value minus the minimum value is less than n Calculate Remaining Button This Button runs the current filter settings to show how many rows will remain after filtering Data Adjustment Options No Data Adjustment This option results in no data adjustment Mean Centering This option mean centers each row of data Median Centering This option median centers each row of data Linear Calibration This option is specific for Affymetrix data and Highly recommended by leading experts in Statistics as applied to DNA data 15 GenePilot V 1 07b August 28 2003 Base Interface Dataset Info Missing Data Imputation Options Nearest Neighbor This option is currently the only miss
76. field Beanh Cancel Search Interface Select Row Information to Search Selecting Visible Fields restricts the search to just the information that is visible as set in the Preferences gt Row Info Display Selecting All Fields causes the search to include all Row Info Fields whether visible or not Select Case Sensitive Checking this box will cause the search to be case sensitive Button Search This Button activates the search Button Cancel This button closes the interface without searching 48 GenePilot V 1 07b August 28 2003 Chapter 5 K Means Clustering Description K Means Clustering is a commonly used unsupervised method for analyzing MicroArray Data It isa top down Clustering method that starts out by randomly distributing the data rows among a preset number of clusters The average vector of each cluster is then calculated then all of the rows are then moved to the cluster whose average vector it is closest to This process is then repeated until either all rows have stopped changing clusters or a few rows are changing back and forth between clusters in a cyclic manner The Vectors for these Clusters is then displayed in the top of the result screen allowing the user to see the vectors for all of the clusters Upon selection of a cluster the vectors for all of it s member rows will be displayed in gray and the cluster average vector will be displayed in it s assigned color In the bottom
77. gene in the currently displayed genes Sort by Selected qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently selected genes Button Select Top This button selects the Gene Ontologies that are at the top of the list in the quantity specified Button Unselect All This button unselects all of the currently selected Gene Ontologies Button Save Changes This button sets the currently selected settings and closes the window Button Cancel This button closes the window without setting any of the changes made 46 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Copy to File Interface Copy to Clipboard Description This Interface allows the user to select which Row Information Fields to include in the Copy to Clipboard and to specify the rows that they want included in the selection Select how much data to copy This section determines which rows will be selected If All Rows are selected then all of the rows in the left panel are copied to the clipboard If Selected Rows are selected If rows are selected in the right panel only those rows will be included Ifrows are displayed in the right panel but no rows are selected all rows displayed in the right panel will be included If no rows are selected in the Left Panel then all rows will be included Select Row Information Fields to include Copy bo Copy te Clipboard Intertace Gehen Per ree
78. gs and running the analytical program Go to SOM Clustering to find out more about the options of this interface Run SAM Action gt SAM This selection is used to bring up the interface for selecting the SAM settings and running the analytical program Go to SAM to find out more about the options of this interface Save Dataset File gt Save Dataset This selection is used to save the current Dataset settings This includes preprocessing settings and settings used by Analytic programs run on the Dataset Select Open Dataset File gt Select Dataset gt Dataset Name This selection is used to select the current Dataset to use when more than one Dataset is open Upon selecting anew Dataset the main window will display the Dataset Info screen Save Settings File gt Save Setup This selection is used to save settings that were used for preprocessing or Analytic runs These settings will become the default settings for future new Datasets For preprocessing the settings will be stored according to the Data Type Url Targets for Row Fields Interface File gt Preferences gt Field Info Urls This selection launches the preferences window for Field Info Target Url View Dataset Heatmap View gt Current Dataset This selection is used to launch a window containing a heatmap of the current Dataset along with row and column information 14 GenePilot V 1 07b August 28 2003 Base Interface Data Adjustment Settings View Dataset Info Vi
79. h experiement This Vector can then be used by GenePilot to do a sophisticated combine of the replicate columns This information can also be used in sorting the columns in the result displays for all of the analytic programs Select Row Type This selection sets the type of data that is represented in each row The following types are available Other This is for types of data which is different from the listed types gene This is for when the rows are genes drug This is for when the rows are drugs 6 GenePilot V 1 07b August 28 2003 Getting Started Creating Dataset Templates Select Number of each type of Vector This selection sets the quantity of each type of vector that will be included with the Dataset Itis recommended that each Dataset have at least one Classification vector included in order to fully utilize the power of GenePilot The following types of Vectors are as follows Classification This vector defines the Class i e Breast Lung for Cancers of each column of data Shape This vector type defines a shape or vector i e expression values of a row Pairs This vector type matches column pairs 1 1 2 2 etc good for before after data Select Row Information Fields to include This selection sets the type of Row Information that will be included in the Dataset Note that GenePilot provides an interface for importing data from an outside source by using some of the ID s Fields with lt Query Field gt can be u
80. he following choices Show All GO Displays all of the Gene Ontologies that are associated with the current Dataset Show only GO from Set Displays the Gene Ontologies that are associated with the currently displayed genes Show only GO from Selected Displays only the Gene Ontologies that are associated with the currently selected genes List Order Choices This selection sets the order that the Gene Ontologies are displayed in the list for selection It has the following choices Sort by name Sorts the Gene Ontologies by their name Sort by Set qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently displayed genes Sort by Selected qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently selected genes Button Select Top This button selects the Gene Ontologies that are at the top of the list in the quantity specified Button Unselect All This button unselects all of the currently selected Gene Ontologies Button Save Changes This button sets the currently selected settings and closes the window Button Cancel This button closes the window without setting any of the changes made 28 GenePilot V 1 07b August 28 2003 Dataset Display Copy to Clipboard File Interface Copy to Clipboard Description This Interface allows the user to select which Row Information Fields to include in the Copy to Clipboard and to also select whether t
81. he user to specify which rows they d like to include in the Copy to File Each Row Information Field that is checked will be included in the copy Button Copy to File This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy a Interface Search AA Description Ender Sear ch Srring This interface is used to set the search term and the settings for the search The search can be restricted to just the visible Row Information or to all Setoct Row informaron no Search Row Information It can also be set to be case sensitive The search C weibieFwids F An Fikes function remembers the last row that it searched in a cluster When a new cluster is selected that information is reset Select Case Senate yes Seach cance Enter Search String i Search Interface The search string is entered into this field Traditional copy and paste methods work on this field Select Row Information to Search Selecting Visible Fields restricts the search to just the information that is visible as set in the Preferences gt Row Info Display Selecting All Fields causes the search to include all Row Info Fields whether visible or not Select Case Sensitive Checking this box will cause the search to be case sensitive Button Search This Button activates the search Button Cancel This button closes the interface without searching 75 GenePilot V 1 07b
82. hes the Create Vector dialog box along with the mean vector of the currently selected rows Gene Ontology Display File gt Preferences gt Gene Ontology Display This selection launches the preferences window for Gene Ontologies Within this preference window the following can be set set number of columns set automatic preferences for selection of Gene Ontologies select specific Gene Ontologies to display Generate Gene Ontology Statistics Action gt Generate GO Statistics This selection launches an html page that contains the statistics for the Gene Ontologies for the rows in the following order of precedence 1 Selectd rows in Right Panel 2 Rows of currently selected cluster in left panel 3 All rows in left panel Launch Info Page Action gt Launch Info Page This selection launches an information page containing a matrix of the genes vs Gene Ontologies if available and a listing of all of the Row Information Fields along with links to websites which have further information 41 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Results Menu Choices Make Dataset Action gt Make Sub Dataset This selection launches and interface that let s the user define criteria for creating anew Dataset from rows of the current Dataset For Hierarchical Clustering there will need to be a cluster selected in the Left Panel Then those rows or the selected rows among those rows can be used as the rows to use in a new Dataset or they c
83. hey want to copy only the selected rows or all of the rows Select how much data to copy This selection allows the user to select whether the rows copied include only selected rows or all rows Select Row Information Fields to include This section allows the user to specify which rows they d like to include in the Copy to Clipboard Each Row Information Field that is checked will be included in the copy Button Copy to Clipboard This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy Interface Copy to File Description This Interface allows the user to select which Row Information Fields to include in the Copy to File and to also select whether they want to copy only the selected rows or all of the rows Select File Path This selection is used to set the path to the output file Click on the Set Output Path to set the file Traditional copy and paste methods work in this field Select how much data to copy This selection allows the user to select whether the rows copied include only selected rows or all rows Select Row Information Fields to include This section allows the user to specify which rows they d like to Copy te Clipboard Interface abel ow reach diate te copy a Eee C Riwi Gebet Fire E cbe Chana iD Untera Symbol LecusLink iD uera Hame 7 Burmary Fonction D Came Crin annotare nr Raphiiantmtea
84. hich defines the color coding for the Class Indication row Actions 1 Clicking and dragging on the bitmap will select those rows 2 Holding down the shift key and selecting a row will extend the row from the previous selection down to the selected row This can be used to select rows in a group that is larger than those seen on the screen 3 When user selected gene ontologies are displayed the Gene Ontology displays can be reverted back to automatic mode by clicking on the Gene Ontology Names Results Menu Choices Bitmap from All Action gt Save All to Bitmap This selection creates a gif bitmap containing all of the information in the Lower Panel Bitmap from Graph Action gt Graph to Bitmap This selection saves the current Graph to a gif bitmap 53 GenePilot V 1 07b August 28 2003 K Means Clustering Menu Choices Bitmap from Selected Action gt Save Sel to Bitmap This selection creates a gif bitmap containing all of the information in the Lower Panel If All Clusters are selected the bitmap will contain the Average Vectors of the clusters If a cluster is selected and rows are selected then only the selected rows will be included in the bitmap If a clusteris selected and no rows are selected the entire contents of the lower panel will be included in the bitmap Copy to Clip Action gt Copy to Clip This selection launches an interface for copying all or selected rows to the clipboard This interface also allows for sele
85. ification Vector s there will be Class Information which defines the color coding for the Class Indication row Actions 1 Clicking and dragging on the bitmap will select those rows 2 Holding down the shift key and selecting a row will extend the row from the previous selection down to the selected row This can be used to select rows in a group that is larger than those seen on the screen Dataset Display Menu Choices About Help gt About This selection shows the about screen for GenePilot Bitmap from Selected Action gt Save Sel to Bitmap This selection creates a gif bitmap containing all of the information specified by the selected rows Bitmap from All Action gt Save All to Bitmap This selection creates a gif bitmap containing all of the information in the Left Panel Copy to Clip Action gt Copy to Clip This selection launches an interface for copying all or selected rows to the clipboard This interface also allows for selecting the Row Information Fields which the user is interested in 23 GenePilot V 1 07b August 28 2003 Dataset Display Dataset Menu Choices Copy to File Action gt Copy to File This selection launches an interface for copying all or selected rows to a file This interface also allows for selecting the Row Information Fields which the user is interested in Create Vector Action gt Create Vector This selection launches the Create Vector dialog box along with the mean vector of the currently selecte
86. in the heatmap panel below 51 GenePilot V 1 07b August 28 2003 K Means Clustering Heatmap Panel Results Parts Heatmap Panel n ERE mim MhMelenama dnt ew st td Ee ELIET TE BLung Cancer Tp OSScow ciui cdm xa WCNS GGGPCGES Y PETETA 22 Sao El JM Colon Pree gt Woe pn o SuPReZe Owarian Er coll oed e a a mELESScgE vaa m m rd oooono uu ug ce ce cece AMS mnagdu BNRenal C a mn a a ESTs 5 36 H20008 BM Homo sapiens thrombospondin 3 THBS3 om GRO GROZ oncogene Chr 4 03 74 Dh clone pj EIE 470934 ueA a ESTs We akly Zimilar to HYPOTHETICAL AMSS Annexin WII Chr d0 B76634 chy BEN Human microfibril associated glycoprotein sp IL1B Interleukin 1 beta Chr z 824655 D TS A AD 3 17 35 SAAS 17 36 7 Wl Hurm an mRNA for FEL ODDS 7 gene compl Dataset Display Heatmap 1 Heatmap 2 Column Information 3 Class Indication when avail 4 Gene Ontology Names when avail 5 Gene Ontology Indication when avail 6 Row Information 7 Class Information when avail Description This panel contains information about the current rows either in the current cluster or about the average heatmap for each cluster The central part is the Heatmap which contains colors from the Palette to indicate values of each row or cluster When Classification Vector s are available a Class Indication row which indicates the classes of each column above the Average Heatmap At the top is the Column Info in the
87. ing data imputation method offered with this software package Dataset Info Panel Description This display shows information about the current Dataset and allows the user to quickly access saved results and delete Dataset and saved results Information Panel This Panel displays the information about this dataset that was either contained in the input template Information field or it was entered into the Information field when a sub Dataset was created from a result window Results Panel This Panel lists the saved results from analytic runs From this panel a saved result can be launched for viewing or can be deleted Graph Panel This panel shows a graphical representation the values contained in a Dataset It shows the distribution of values 16 GenePilot V 1 07b August 28 2003 Base Interface Row Info Import Button Panel This panel contains buttons for acting on the Dataset These are the current Buttons Import Row Info From Internet Launches interface for Row Info Import Delete Dataset Deletes the current Dataset Interface Row Info Import Description This interface provides the steps to import additional Row Information from the Stanford Source Website which can greatly enhance the information that can easily be displayed in GenePilot Thereis a H TT SE om large selection of information that GenePilot can ree handle including Gene Ontology information The only requirement is that the dataset alread
88. ining if necessary from most common among remaining rows in the current delta range Auto Delta Range Chooses most common Gene Ontologies among the rows displayed for the current delta range User Select Displays rows that the user has specifically selected This gets turned off when the user clicks on the Gene Ontology Names Select or View Gene Ontology Entries This section is for viewing or selecting specific Gene Ontologies by checking the checkbox either manually or using the Select Top button under the list List Show Choices This selection sets the Gene Ontologies that will be displayed in the list for selection It has the following choices Show All GO Displays all of the Gene Ontologies that are associated with the current Dataset Show only GO from Delta Range Displays the Gene Ontologies that are associated with genes from the current delta range Show only GO from Selected Displays only the Gene Ontologies that are associated with the currently selected genes List Order Choices This selection sets the order that the Gene Ontologies are displayed in the list for selection It has the following choices Sort by name Sorts the Gene Ontologies by their name Sort by Delta Range qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently delta range Sort by Selected qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently selected genes
89. ins the grid of nodes Each node contains a small graph of the node vector in the middle and a bar along the left that M M7 indicates the number of member rows In reference to a node the first i E oe column is 0 and the first row is 0 To the right of the Nodes is the we Legend which gives information on the nodes and indicates which node is eS ce ae Pag cere currently selected The currently selected node will have it s borders um a Sal d SOM Hexagonal Nodes colored in green Nodes Left The nodes are either square or Hexagonal depending on the Grid Type selected Within each node is a small graph in red representing the node Vector On the left side of each node is a blue bar representing the number of rows associated with this node this node having the vector which was closest to each row vector 64 GenePilot V 1 07b August 28 2003 SOM Heatmap Panel Legend Right The upper portion of the Legend serves as a legend for the node panel In the lower part is text indicating to Click node to select deselect if no node is currently selected or the coordinates of the node 0 based if a node is selected Actions 1 Clicking on an unselected node will select that node as the current node 2 Clicking on a selected node will unselect it Results Parts Heatmap Panel Description This panel contains the specific information for the rows or nodes The central part is the Heatmap which c
90. le gt Open gt Dataset Name This selection is used to open a Dataset that has already been loaded into the system Once GenePilot has opened the Dataset the main window will display the Dataset Info screen Pre Process Settings Action gt Pre processing This selection is used to view the preprocessing settings for this Dataset This is where the Filtering Data Adjustment and Missing Data Imputation selections are made Go to Pre Processing section to find out more about the options of this interface Quit File gt Quit This selection is used to quit out of GenePilot 13 GenePilot V 1 07b August 28 2003 Base Interface Menu Choices Row Info Display File gt Preferences gt Row Info Display This selection is used to set the Row Information fields that will be displayed as Row Information to the right of the Result Heatmap Run Hierarchical Action gt Hierachical This selection is used to bring up the interface for selecting the Hierarchical Clustering settings and running the analytical program Go to Hierachical Clustering to find out more about the options of this interface Run K Means Action gt K Means This selection is used to bring up the interface for selecting the K Means Clustering settings and running the analytical program Go to K Means Clustering to find out more about the options of this interface Run SOM Action gt SOM This selection is used to bring up the interface for selecting the SOM Clustering settin
91. ll rows owned by the cluster represented by anode The selected rows will be displayed in the right panel 3 Holding down the shift key and selecting a row will extend the row from the previous selection down to the selected row This can be used to select rows in a group that is larger than those seen on the screen The selected rows will be displayed in the right panel 38 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Results Menu Choices Results Parts Right Panel FE E Melenama 0 Ekeng Canes a Colon 8 OW OC AR EU Tix E MEI i Mer marniiana fraction rebel pmino acid pharpho LE CCRF CEM LC NCI MX22 NM LE HL A5 LC HCLHA22 LC NCIMZX CO COLOZUS CO HCC 2898 COHTz9 Oy OCR ME WAC C25 OW SK OW ORO CUO HCT 1185 BR TD BRIMCEFT CO 5w 820 CO HCT 15 LE MOLT 4 iO Kren integral io membrana zi zignaltransductisn niackeug plasma ma a Lo E fh 5 2 x m APTA ApS phesir APO 4 antigen 1 Chr A0 ESTs P R2 1720 GRO eee Human exta cinane splice wanani 1 mane Neuronal pardrxsin I eH ia a F H00 ESTs Ei FASE LJ ESTs P HHS 2 N39352T mm m Human mRNA for AACS gene compl EEST 5 3 N87 4587 EN H WP reiein kinace C mu E 3 NB4058T Results Right Panel 1 Heatmap 2 Average Heatmap 3 Column Information 4 Column Dendigram 5 Gene Ontology Descipriptions 6 Gene Ontology Indications 7 Row Infor
92. lot V 1 07b August 28 2003 SOM Copy to Clipboard F ile Interface Copy to Clipboard DNETIEDTUNITETUTEESS oid Copy te Clipboard Interface Sekeni how uocis dotado copy LETT TIIT m Description This Interface allows the user to select which Row Information Fields to include in the Copy to Clipboard and to specify the rows that they want included in the selection Cinna is Unite Symbol Select how much data to copy LeeusLinikciD This section determines which rows will be selected When All Rows is usitess ame selected then all of the rows in the current node are copied to the 9 tumar F unesen clipboard or all nodes along with their rows are copied if no node is D Gana CrtniogrAnnctatiom selected When Selected Rows is selected If rows are selected in the Representitvs mRNA Acc Heatmap only those rows will be included If a node is selected but no WB ls rows are selected all rows in that node will be included If no node is LIE selected then all nodes along with their rows will be copied Serio Cipbant cams Copy to Clipboard Interface Select Row Information Fields to include This section allows the user to specify which rows they d like to include in the Copy to Clipboard Each Row Information Field that is checked will be included in the copy Button Copy to Clipboard This Button Initializes the copy and closes the window Button Cancel This But
93. map is a column indicating Correlation and the FDR To the far right of the Heatmap is the Row Information which contains the description of the row In the top right corner the legend for the Class Indication will define the colors for each class when Classification Vector s are available When the Delta is set to it s largest value there will be few rows displayed As the Delta value is lowered more rows will be added as the significance requirements are relaxed Heatmap Bottom Left The heatmap contains rectangles color coded in the Palette colors to represent the value of each cel juncture of 1 row and 1 column By default these colors are Red highest value and Green lowest value When No Normalize is selected the value range is defined by the min and max values in the entire Dataset Rows remaining after filtering with zero being the medium value When Normalize is selected then the value range for each row is defined by the min and max values in that row with the mean value being the medium value 79 GenePilot V 1 07b August 28 2003 SAM Heatmap Panel Class Indication Above Average If there is Classification Vector s there will be Class Indicators above the Heatmap This is a row of rectangles which are color coded to indicate the class of each column as defined by the Class Information block in the Top Right corner Column Names Upper Left The Column Information contains the column names rotated counter clo
94. mation 8 Class Information Not Shown gt Class Indication o Description This panel contains the specific information for the current cluster that has been selected in the Left Panel The central part is the Heatmap which contains colors from the Palette to indicate values of each row or cluster Above the Heatmap is the Average Heatmap a single row heatmap that indicates the average vector of the current cluster When Classification Vector s are available and there was no column clustering a Class Indication row which indicates the classes of each column is above the Average Heatmap Above all ofthis is the Column Info in the form of text rotated counter clockwise by 90 degrees If the columns have been clustered the Column Info is topped by a dendigram of the column clustering which is either black or color coded depending on if Classification Vector s are available To the right of the Heatmap is the Gene Ontology indication when Gene Ontology information has been imported into GenePilot for this Dataset To the right is the Row Information which contains the description of the row In the top right corner the legend for the Class Indication will define the colors for each class when Classification Vector s are available Heatmap Bottom Left The heatmap contains rectangles color coded in the Palette colors to represent the value of each cel juncture of 1 row and 1 column By default these colors are Red highest value
95. miRTA Ae Repneemtates Protein Arc riba Chuster iD Copia Carboard Cancel Copy to Clipboard Interface By La File information Tsj Copy to File intertace Seto File Batic Drit Fgenepuens det ip bi Gea Guipel Path Select how mach dara ta cope Of Galeries ow C M Ren Kekit Fare fo rruareon Fihi Da rac kucke 7 cione ID T Ueiena gmba F LaeusLink it Uei ese Name F Susman Feman Gans Oreciogs kanamin fapuaxanumme inf AE V pepara Proton Acc Leiden Cedar at asi Copy to File Interface include in the Copy to File Each Row Information Field that is checked will be included in the copy 29 GenePilot V 1 07b August 28 2003 Dataset Display Row Information Window Button Copy to File This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy Interface Search Description This interface is used to set the search term and the settings for the search The search can be restricted to just the visible Row Information or to all Row Information It can also be set to be case sensitive Enter Search String The search string is entered into this field Traditional copy and paste methods work on this field Select Row Information to Search i 8 s Search Interface Enter Search Saving m Rekoa Firei infeirnarnion no Susan ch webleFudds F AN Fikes Select Case Sense ves Seach cance Search
96. n SOM read more about it in Significance Analysis of microarrays applied to the ionizing radiation respons Reference 1 V Tusher et al 76 GenePilot V 1 07b August 28 2003 SAM Run Settings Run Settings fuppetvecter Caner gt Fun each chent egies Mi oe ETE RT SAM Run Settings Panel Description The Run Settings provide a means to alter the way that SAM Analyzes the Data The primary action to make is to select the Support Vector that will be used by SAM It is recommended to Run each classification against all others if a classification vector is selected This will take longer to run but will provide a wealth of information well beyond that given by a single run when more than two classes are present Support Vector This selects the vector to be used by SAM Run each classification against all others If the selected vector is a Classification vector and this selection is checked SAM runs more than one time In the first run the Classification Vector is used Then for each class as vector is generated where the current class retains it s classification and all other classes are grouped together This finds significant rows which are specific to a single class Button Run This button runs the K Means Clustering analytic program Button Reset This button resets the values to the last saved values Button View Saved Result This button is only present when a previous result has been saved Clicking on
97. name MON NOE EA can bet set to anything as long as the name is not gana Eee as already in the system ES ej Crete Dates caeca Hamp Select Columns to Include Default All The button Select Columns launches a window that allows for selection of the columns to be included in the new Dataset If no column selection is made then all columns will be used Set New Dataset Info This text field is the Dataset information field It is seeded from the result Dataset Information Additional information should be added here to provide a pedigree for the new Dataset Set Whether to Include or Exclude Selections When Include is selected only the rows designated will be used in the new Dataset When Exclude is selected the rows designated will be subtracted from the rows that made it through the filtering process if any to create a new Dataset Select Check Boxes These check boxes give the option to select each node to be used for defining the rows to be included or excluded Use Selected Check Box This check box is only available for the current node When checked only the selected rows will be used It is only shown when rows are selected in the heatmap Button Select All This button checks all of the Select Check Boxes making it more convenient to select most of the nodes 70 GenePilot V 1 07b August 28 2003 SOM Row Info Display Settings Button Clear All This button clears all of the Select Check Boxes making it
98. nePilot V 1 07b August 28 2003 SAM Row Info Display Preferences Use Selected Check Box This check box is only available for the current run When checked only the selected rows will be used It is only shown when rows are selected in the heatmap Button Select All This button checks all of the Select Check Boxes making it more convenient to select most of the runs Button Clear All This button clears all of the Select Check Boxes making it more convenient to turn off selection of most or all of the runs Button Create Dataset This button creates the Dataset once all of the settings are made Button Cancel This button closes this interface without creating the new Dataset Preferences Row Info Display j Row inte Fiala Selection Panal Select pepo cha Description The Row Info Display Preferences Window is used to specify the Row Information fields that will be displayed to the right of the Heatmap In addition to selecting the fields the field order can be specified foes along with the character seperating the contents ofeach gane coros Annotations field Fields are selected for inclusion by moving them Fepeesantutive MANA Acc from the left column Available over to the right Fepeesarfative Protein An column Included The order of display is set by their 055 userin row order with the first row being the first display field LniGasnis Gymbol Lacus Lin r ID se Make Changer caeca Select separa
99. ng Data Input Data Rows lt Required gt These rows contain the Data The following describes the entries needed Column 1 Row Name Defines the name of this row i e gene name gt Shown in result windows with Information Column 2 Identifier Defines the Identifying number preferably the Accession number for this row Column 3 Information Defines the information that you wish to see displayed in the results window next to each row Column 4 Weight If no specific weight set to 1 or leave blank Column 5 to n Column Value Any value but don t use scientific notation 11 GenePilot V 1 07b August 28 2003 Chapter 2 Main Window Description The main window is the control window for GenePilot From this window Datasets can be uploaded selected closed or saved Preprocessing settings can be set information for datasets can be viewed and analytical runs can be configured The purpose of this window is to control the process of Analyzing MicroArray Data Following is a description on how to navigate through the process of Analyzing data with GenePilot 12 GenePilot V 1 07b August 28 2003 Base Interface Menu Choices Menu Choices Archive Dataset File gt Dataset gt Create Archive This is used to Save the Dataset the settings used for preprocessing and the analytics and the saved results All of this information is stored in pkzip format to save room for storage This format is also
100. ng replicate Columns using a variety of methods and to also exclude the Rows with bad Data from the resulting Dataset A display showing the quality of the combined data measured by SD Mean of the combined data for each row column combination Row information is included in order to see which rows have the bad or good data Those rows can be sorted in two ways and a block of rows can be selected to exclude 18 GenePilot V 1 07b August 28 2003 Base Interface Replicate Column Combine Column and Row Statistics Display On the right hand side of the interface is a display which shows the quality of the replicates in relation to the other columns The combined column Name Name of first column in each set is displayed at the top To the right of that is the legend defining the colors used in the Heatmap The Heatmap utilizes the colors to indicate the quality of the combined values To select rows click and drag If more rows than can be displayed at once need to be selected page down to ending row and select that row while holding down the sshift key this will extend the selection down to the selected row To the right of the Heatmap is the Row Information Clicking on a row in this section will bring up an information window with all loaded information about that Row Set Name for Combined Dataset This field is for setting the new name of the combined Dataset By default Comb is added to the name of the current Dataset Not th
101. nks to websites which have further information Make Dataset Action gt Make Sub Dataset This selection launches and interface that let s the user define criteria for creating anew Dataset from rows of the current Dataset For SAM the FDR or selected rows can be used to determine rows to be included or excluded from the new Dataset If a classification vector was used and multiple runs was selected then one or more runs can be used to determine the rows to be included or excluded Selected rows in the current run can also be used Quit File gt Quit This selection closes the Result Window Save Results File gt Save Results This selection is used to save the current result This will save the results of an Analytic run so that the results can be viewed immediately Once an analytic result is saved for a Dataset a button will be added to the Dataset Information screen to quickly view the saved result Search Action gt Search This selection launches the search interface which allows the user to search the rows for a String See Search Interface for more information on the Search Interface For K Means Clustering the search will search the currently selected cluster first it will then continue the search through the remaining clusters then start over at the beginning cluster Search Again Action gt Search Again This selection searches for the next case of the search string Select Classification Vector If Avail Classes gt
102. ntology Statistics 68 Grid size 63 Grid Type 63 Heatmap Panel 65 Initial Seed Type 64 Initial Size of Neighborhood 63 Launch Info Page 68 Make Dataset 68 T U V 96 Menu Choices 67 Neighborhood Type 63 Node Panel 64 Normalize Rows 69 Number of Iterations 63 Palette 31 Quit 68 Row Info Display 71 Row Information Page 32 Row Information Window 31 33 Run 14 Run Settings 63 Save Results 68 Search 68 75 Select Palette 69 Show Palette 69 Summary Function Creating Dataset Templates 7 Support Vector SAM 77 Tutorials Sample Data 5 Your Data 5 UniGene Cluster ID Creating Dataset Templates 7 UniGene Name Creating Dataset Templates 7 UniGene Symbol Creating Dataset Templates 7 Url Lookup Editor Dataset Display 33 Vectors Classification Vector 10 Pair Data 10 Preparing Data 10 Replicates Vector 9 Shape Vector 10 GenePilot V 1 07b August 28 2003
103. o the left column up This button moves the currently hilited field in the right column up one row down This button moves the currently hilited field in the right column down one row Button Make Changes This button must be clicked in order for the changes to be made Button Cancel This button cancels any changes that were made and closes the window 71 GenePilot V 1 07b August 28 2003 SOM Gene Ontology Preferences Preferences Gene Ontology Description This interface is used to set the Gene Ontology preferences for this screen The choices include automatic selection of the most common Gene Ontology categories based upon either the currently selected rows or for all rows in the current node If the selected rows have preference and there aren t enough categories to fill the number of columns then the most common categories across all rows in the node are used to fill in the categories Specific Gene Ontology categories can also be specified this is aided by the List Show Choices and List Order Choices for quickly finding specific Gene Ontologies Select Number of Gene Ontology Columns to show This selection sets the number of columns that will be displayed Select GO Types in Display fe acter Wslik Setlinegs Cana Ontelegy Settings Panel Select Mumbar of Gore Crisiogy Columm taster UN Sete Can Tapes io Debs plos ae C Auto Cupar C Uer Select Sebel comio E Aata Dalachya Saket or Wis
104. og box along with the mean vector of the currently selected rows Gene Ontology Display File gt Preferences gt Gene Ontology Display This selection launches the preferences window for Gene Ontologies Within this preference window the following can be set set number of columns set automatic preferences for selection of Gene Ontologies select specific Gene Ontologies to display Generate Gene Ontology Statistics Action gt Generate GO Statistics This selection launches an html page that contains the statistics for the Gene Ontologies for the rows in the following order of precedence 1 Selectd rows in Right Panel 2 Rows of currently selected cluster in left panel 3 All rows in left panel Display All Data Display gt All Data This choice selects all Data to be displayed which includes Correlated Data and Anti Correlated Data Display Correlated Data Display gt Correlated Data This Choice selects only Correlated Data to be displayed Anti Correlated data will be excluded from the display 81 GenePilot V 1 07b August 28 2003 SAM Menu Choices Display Anti Correlated Data Display gt Ani Corr Data This Choice selects only Anti Correlated Data to be displayed Correlated data will be excluded from the display Launch Info Page Action gt Launch Info Page This selection launches an information page containing a matrix of the genes vs Gene Ontologies if available and a listing of all of the Row Information Fields along with li
105. ontains colors from the Palette to indicate values of each row or cluster To the top of each column is the Column Info in the form of text rotated counter clockwise by 90 degrees A row of rectangles which are n Ens mim BMhielenoma dnt ew ed Se ezE ELung Cancer STO Ego c IGI cam uab NCNS GocpU SEDES QEV Re 20 aD E mCalen Sern e e E omaZ22E mo PE rnEeE A EE lle cian oooongmuu ug oe oe oe AMSmaHAw NRenal E Eum gau ESTs 5 36 H20008 E Homo sapiens thrombospondin 3 THBS3 om GRO GROZ oncogene Chr 4 80971 Dh clone pj Gc m eTSID 470934 pAAA SS ESTs We ak imilar to HYPOTHETICAL AAO Annexin WII Chr 10 B76634 chy BEN Human microfibril associated glycoprotein E 505 IL1B Interleukin 1 beta Chr z 24655 D TS AAS 17 35 SAAS 17 367 m m Wl Hum an mRNA for ELA OO 37 gene compl Dataset Display Heatmap 1 Heatmap 2 Column Information 3 Class Indication when avail 4 Gene Ontology Names when avail 5 Gene Ontology Indication when avail 6 Row Information 7 Class Information when avail color coded to indicate the class of each column will be in between the Heatmap and the Column Info when Classification Vector s are available To the right of the Heatmap is the Gene Ontology when available indications To the far rightis the Row Information which contains the description of the row In the top middle is the Gene Ontology descriptions when available In the top right corn
106. opular and widely used tools with features that greatly enhance the ability of the user to datamine their information It is simple enough to use for any user to feel comfortable in using most of it s features within a half hour This contrasts with most of the popular tools that are currently available which are quite confusing for even veterans at MicroArray Analysis To get started it is recommended that the user start with one of the sample Datasets The first is a sample of a cDNA Dataset from the NCI Itis based on the NCI T Matrix Dataset and has very interesting results It can be found in the Sample Data folder and it s name is NCI_T_Matrix txt 1 GenePilot V 1 07b August 28 2003 Getting Started Installation Installation Windows Instructions Instructions After downloading double click GenePilot_v1b exe Notes If you do not have a Java virtual machine installed be sure to download the package above which includes one Mac OS Classic 8 1 or greater Instructions Instructions After downloading double click GenePilot_v1b exe Notes Requires PowerPC and Mac OS 8 1 or later You may need to install Mac OS Runtime for Java MRJ 2 2 or later before using this package The installer is MacBinary encoded and should be automatically decoded after downloading If itis not automatically decoded you can decode it using StuffIt Expander 4 5 or later Mac OS X Instructions Instructions After downloading double
107. oup this column is part of 9 GenePilot V 1 07b August 28 2003 Getting Started Preparing Data Input Vectors Classification Vector lt Optional Recommended gt This entry defines the class which each column is associated with With a Dataset with Cancer data this could be Breast Lung Melanoma etc This class information can be selected and displayed under each column name for every Analytical result which can prove extremely useful in understanding the results You can define and include as many different classification vectors as you wish All Vectors must be in the rows immediately following the Column Names row The following describes the entries needed Column 1 leave blank Column 2 Vector Type Must begin with Class Column 3 Vector Name Defines the name of the vector used throughout GenePilot First Data Column to last Name of the Class Make sure it s identical to others of same type i e Breast Lung etc Input Vectors Shape Vector Optional This entry defines the Shape Vector associated with this Dataset This can be a vector from one of the rows or a cluster of rows it can be the time or any other set of numbers that define a shape that may be used to analyze the data You can define and include as many different Shape vectors as you wish All Vectors must beinthe rows immediately following the Column Names row The following describes the entries needed Column 1 leave blank Col
108. rarchical Clustering 41 K Means Clustering 53 SAM 81 SOM 67 Bitmap from Graph K Means Clustering 53 Bitmap from Graphs SAM 81 Bitmap from Grid SOM 67 Bitmap from Selected Dataset Display 23 Hierarchical Clustering 41 K Means Clustering 54 SAM 81 SOM 67 C Chromosome Location Creating Dataset Templates 7 Class Indicator Hierarchical Clustering 40 K Means Clustering 52 91 SAM 80 SOM 66 Class Information Hierarchical Clustering 40 K Means Clustering 53 SAM 80 SOM 66 Classification Vector Creating Dataset Templates 7 Clone ID Creating Dataset Templates 7 Col Similarity Metric 36 Column Dendigram Hierarchical Clustering 40 Column Info Hierarchical Clustering 40 Column Names K Means Clustering 53 SAM 80 SOM 66 Copy to Clip Dataset Display 23 Hierarchical Clustering 41 K Means Clustering 54 SAM 81 SOM 67 68 Copy to Clipboard Interface Dataset Display 29 Hierarchical Clustering 47 K Means Clustering 60 SAM 88 SOM 74 Copy to File Dataset Display 24 Hierarchical Clustering 41 K Means Clustering 54 GenePilot V 1 07b August 28 2003 Index SAM 81 SOM 67 Copy to File Interface Dataset Display 29 Hierarchical Clustering 47 K Means Clustering 60 SAM 88 SOM 74 Correlation and FDR Column SAM 80 Create Dataset Hierarchical Clustering 43 K Means Clustering 56 SAM 84 SOM 70 Create Vector Dataset Display 24 Hierarchical Clustering 41 K Means Clustering 54 SAM 81 SOM 67 Creating
109. relationships between the enctegeneebunsita prece Eua Peden al Ton eT eo mE ees Ga 0 5234 prora selected genes and the Gene Ontology Categories _ M srsestater sles Ace nia nna 3 ae Aepresenaier Protein Acc MP 478904 when Gene Ontology information is imported or recane cioe ite n orat loaded and links to additional information Additional Information Row formation Window When a Row Information window is launched a reference gets added to the Window menu Multiple instances of this window can be launched at the same time which each new one getting a unique number in order Selecting this window from the Window menu will bring it to the front Traditional copy methods should work on all platforms i e lt ctrl gt c on Windows to allow for copying and pasting into another program Common Windows Palette i Current Palette min med max Heatmap Palette Window Description The Palette Window displays the palette that is being used by the Heatmap When Normalize is selected the min and max colors represent the min and max values for each row When Normalize is not selected then the medium value is 0 and the min and max values are determined by the Absolute maximum value on either side of zero if the lowest value is 3 and the largest value is 5 then min will be equal to 5 and max will be equal to 5 31 GenePilot V 1 07b August 28 2003 Dataset Display Row Information Page Common Page Row Information Page
110. ring 56 SAM 83 SOM 69 Filter View 13 Filtered Data Show 26 Filtering Options 15 Min Max 15 Negative Values 15 Observations 15 Percent Present 15 Standard Deviation 15 G GenBank Accession Creating Dataset Templates 7 Gene Aliases Creating Dataset Templates 7 Gene Ontology Dataset Display 23 Hierarchical Clustering 40 K Means Clustering 53 66 SAM 80 Gene Ontology Anotations Creating Dataset Templates 7 Gene Ontology Display Dataset Display 24 Hierarchical Clustering 41 K Means Clustering 54 SAM 81 SOM 67 Gene Ontology Settings K Means Clustering 58 SAM 86 SOM 72 Gene Ontology Statistics Dataset Display 24 Hierarchical Clustering 41 K Means Clustering 54 SAM 81 SOM 68 GenePilot Field Info Url Targets Interface 14 Grid size SOM 63 Grid Type SOM 63 H Heatmap Hierarchical Clustering 39 K Means Clustering 52 SAM 79 SOM 66 Heatmap Panel K Means Clustering 52 SAM 79 SOM 65 Help Dataset Display 24 Hierarchical Clustering 35 Bitmap 41 Copy to Clipboard 41 Copy to Clipboard Interface 47 Copy to File 41 Copy to File Interface 47 Create Dataset 43 Create Vector 41 Field Info Url Targets Interface 43 Gene Ontology 40 Gene Ontology Display Settings 41 Gene Ontology Statistics 41 Launch Info Page 41 Left Panel 37 Memory Model 37 Palette 31 Quit 42 Results Menu Choices 41 Right Panel 39 Row Info Display 44 Row Information Page 32 Row Information Window 31 33 Run 14 Run Settings 36 Save Results 42
111. rotein An row order with the first row being the first display field cus Select separator char This selection sets the character that will separate the information from each field Row Info Field Selection Panel Select Row Info Fields This section allows for selection of the specific fields that will be displayed in the row info and the order of these fields It has the following buttons gt gt This button moves the currently hilited field in the left column over to the right column lt lt This button moves the currently hilited field in the right column over to the left column up This button moves the currently hilited field in the right column up one row down This button moves the currently hilited field in the right column down one row 44 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Gene Ontology Preferences Button Make Changes This button must be clicked in order for the changes to be made Button Cancel This button cancels any changes that were made and closes the window Preferences Gene Ontology Description This interface is used to set the Gene Ontology preferences for this screen The choices include automatic selection of the most common Gene Ontology categories based upon either the currently selected rows or for all rows If the selected rows have preference and there aren t enough categories to fill the number of columns then the most common categories across
112. roughly determined by the height of the node that binds the two entities columns or clusters together Gene Ontology Names Middle Right If Gene Ontology Information The Gene Ontology Names is a variable column display that displays the Gene Ontology Names that are currently chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set If specific Gene Ontologies are selected by the user the settings can be easily changed back to automatic selection by clicking on this Gene Ontology Names display Gene Ontology Indication Bottom Middle The Gene Ontology Indication indicates the Gene Ontologies that are associated with each row The Gene Ontologies are chosen either automatically Most common in dataset or most common in selected rows or by the User Using File gt Preferences gt Gene Ontology Display these different choices can be set Row Information Bottom Right Row information contains the row name and row information to the right of each row in the heatmap Class Information Top Right If Class Vector Ifthere is Classification Vector s there will be Class Information which defines the color coding for the Class Indication row Actions 1 Clicking and dragging on the bitmap will select those rows 2 Holding down the shift key and selecting a row will extend the row from the previous selection
113. sartatvn Progen Acc ieiuna inia i Copy to File Interface GenePilot V 1 07b August 28 2003 Hierarchical Clustering Search Interface Select how much data to copy This section determines which rows will be selected If All Rows are selected then all of the rows in the left panel are copied to the file If Selected Rows are selected If rows are selected in the right panel only those rows will be included If rows are displayed in the right panel but no rows are selected all rows displayed in the right panel will be included If no rows are selected in the Left Panel then all rows will be included Select Row Information Fields to include This section allows the user to specify which rows they d like to include in the Copy to File Each Row Information Field that is checked will be included in the copy Button Copy to File This Button Initializes the copy and closes the window Button Cancel This Button closes the window without doing the copy Interface Search Description Zowuh UTI 5 This interface is used to set the search term and the settings for the search Enter Snarch Siring The search can be restricted to just the visible Row Information or to all p T Row Information It can also be set to be case sensitive aisi ow Iniarmation bs Search C weibleFw dy S AFi Enter Search String The search string is entered into this field Traditional copy and paste E L methods work on this
114. sed for importing additional information This allows for importing minimal information then populating the dataset with a significant amount of information through the Data import process fields with lt Import Item gt are fields that can be imported GenePilot supports the following information Clone ID lt Query Field gt lt Import Item gt Commonly used in NCI Data CLID GenBank Accession lt Query Field gt lt Import Item gt UniGene Name lt Query Field gt lt Import Item gt UniGene Symbol lt Query Field gt lt Import Item gt LocusLink ID lt Query Field gt lt Import Item gt Chromosome Location lt Import Item gt Gene Aliases lt Import Item gt UniGene Name lt Import Item gt Summary Function lt Import Item gt Gene Ontology Annotations lt Import Item gt Representative mRNA Acc lt Import Item gt Representative Protein Acc lt Import Item gt UniGene Cluster ID lt Query Field gt lt Import Item gt Enzymatic Function lt Import Item gt Misc or Orig Desc Suggested field for description information included with Original data Button Create Template This button creates the template Button Cancel This button closes the window without creating the template 7 GenePilot V 1 07b August 28 2003 Getting Started Preparing Data Preparing Data Mame Dataset Name o Type of Data C S Model Number 1 n a Row Type 0 i 1 0 Lead Col Count 3 e amp Information
115. sscesesssssse 74 Interface Copy to File cH 74 Interface SCI assesses ease cetiowe cen REL ebeH FIOR IM essees sees Ise EEE EOS osses Eroii 75 C napteE T SAM seticsivccunaciten 1 O Run SECS eee 77 Results Parts EDR Graph cicteccsdcsssccsccsscecscsessactacavcatcacescstvessonstetitesccsenetivescecsstete 78 Results Parts Score Graph ssssececsssosececessoocecesssccocessosseceesesooececessooeesesssessssee 78 Results Parts Heatmap Panel seseesssoocssessssocccessssooeccesoosoceessoscccsssscsosesssssssesseo 79 Results Menu Choices P T 81 Windows Cr ate Dataset wsissscestisccesscssccaxosscanscesseanasascssensccuvonsssnecsssedsenenssseseasiasiaes 84 Preferences Row Info Display iot eei esee era pebnac Ia cratetetentenscciesenciciccieteinieseeients 85 Preferences Gene Ontology eT G 86 Interface Copy to Clipboard avsscssscxtcdwccsnsciecenccatscsecencsezenevisucbicceuetetebextncsseieusesecst 88 Interface Copy to Eile e 88 Interface SCA CH MR 89 References eee eee eee eee eee OU MING OX ERR Chapter 1 Getting Started Description GenePilot is a stand alone application designed to provide an intuitive and comprehensive interface for analyzing MicroArray Data It combines the most p
116. st value in the palette will be applied to the highest value in the row the color corresponding to the lowest value in the palette will be applied to the lowest value in the row and all other values will be scaled accordingly Show Rows Un Normalized Normalize gt NoNorm This selection displays the traditional heatmap display where color selections from the palette are determine from the highest and lowest value among the data not just in a row Url Targets for Row Fields Interface File gt Preferences gt Field Info Urls This selection launches the preferences window for Field Info Target Url 69 GenePilot V 1 07b August 28 2003 SOM Create Dataset Windows Create Dataset Bb Crate Cat aiet fram nck T Pain Create Sub Dataset Interface Description Sut Mier Drabass Marre f T ams d FTE Gaim This Interface is used to create anew Dataset by using 5etColummstoinchsdeiDefauR AN Goni Coumans one or more nodes for defining either the rows in the tL new dataset or the rows to be excluded in the new LR ie a PIEZA OEC NE Dataset In the current node the selected rows can be used to further refine the selection zi Sed Whether ti racia ot erhia Koitin Set New Dataset Name wek 9 kek C i This text field is the name that the new Dataset will eae ar rer receive Itis seeded with the result Dataset Name TE along with SOM to indicate that it was created Node rw cnt using the results from a SOM resultscreen That
117. stribution of strength of the influence that a placement in a node has on it s neighbors 1 Gausian Linear weakening of influence with distance from full strength on updated node down to zero strength at current boundary of neighborhood 2 Bubble No weakening of influence within neighborhood Initial Size of Neighborhood This determines the size of the neighborhood at the start With each cycle the Neighborhood becomes marginally smaller until the final placed nodes have no influence on the nodes around them 63 GenePilot V 1 07b August 28 2003 SOM Node Panel Initial Seed Type This determines how the vectors within the nodes are initially seeded 1 Random Rows Each node is seeded with a random row from the Dataset 2 Random Values After calculating the Mean Value and Standard Deviation random values are calculated and placed into each position of the vector for each node Button Run This button runs the K Means Clustering analytic program Button Reset This button resets the values to the last saved values Button View Saved Result This button is only present when a previous result has been saved Clicking on this button will launch the saved result Results Parts Node Panel Legend O Nodes Cur Hade E Sh a Eres in hode s Moda archer Eras Corneal Medea Four d Gal f Che k ente 15 d ilie rd dett SOM Node Panel Square Grid 5 Columns X 5 Rows Description The Node Panel conta
118. t can be customized to exactly fit the needs Select Row Typr C Omar E gene C drag of the dataset avoiding the need to add or delete Tatact ib i each pa ol Vetter rows or columns Once the template is created the cusnsaicamer p m eap s Fev o 7 information can then be filled in See Preparing Data oo enter E es Chon iD DerniBar Accession and loaded into GenePilot The Make Dataset Pin hen Fi Template window can be opened by accessing the omo i oe eeu menu item File gt Dataset gt Create Template n m T Usije Hame Semea Fusctos Gene Oriciogs Annotations Select Dest File oso NL nns in UniGene Chester ID Enzemam Famin This field sets the name and location of the template uc er orig Desc file Click on the Set Path button to select the create Tecum Cancel location and file name Select Data Chip Type Make Dataset Template This selection sets the type of chip used to generate the data The following types are available Other This is for Chip Types that aren t listed cDNA This is for data that is produced using cDNA type chips Affy This is for data that is produced using Affymetrics chips There is one additional field in this selection in the form of a checkbox Call Columns This only applies to Affy data and should be checked if there is columns of Call Data included after each Data Column Include Replicate Column Vector This selection adds in a Vector for specifying replicate columns for eac
119. te existing information checkbox is selected then all Row info fields will be overwritten where the incoming data has valid data if empty field in incoming data then original data if present will remain If the checkbox is not selected then existing fields with valid data will not be overwritten but where these fields are empty valid incoming data will be filled in 17 GenePilot V 1 07b August 28 2003 Base Interface Replicate Column Combine Button Import New Information This Button imports the data into GenePilot Button Cancel This button closes the interface without any additional actions Interface Replicate Column Combine Panel RIETI Fe View Action virki Heb Manr Alha pcm axi Truc Eya Comat tn Chis Type Replicate Column Combing Panel Chaat oer Order 5m Perente uan RH ENEY ENEY TUO UR Mor zs Ate sep sien ken ri LRASRRE IY free TT Ta description Tor Combined Dus an pit eee Te Te DM Eus ct me mpal gene mpeg s sion STE Treg A ee f Bae pee pes nme ae bom vates mause medals ef Saskect typus eif combina I Median Vales Mean Vales wWeigeied lian valus Cheriar what to iocchudar F Eme Selected Rives Crate Comrad Diipa Replicate Column Combine Panel Description Heri a poA gairi TSS iTi 3 Ta Wu ay ansia t Bred aibh IIN mktaba iens Md Li LS ITI ET IER a Aa Tal pales M This interface allows for combini
120. the heatmap and related information will be displayed so that the member rows and information can be examined For more information on K Means Clustering read more about it in Cluster Analysis for Large Scale Gene Expression Studies Reference 5 A Sturn 49 GenePilot V 1 07b August 28 2003 K Means Clustering Graph and Button Panel Description Run Settings Murmber af Clusters i 0 Run settings provide a means to effect the number of clusters that are used Run Reset View Saved Result Number of Clusters This selection determines the number of clusters to be used Button Run This button runs the K Means Clustering analytic program Button Reset This button resets the values to the last saved values Button View Saved Result This button is only present when a previous result has been saved Clicking on this button will launch the saved result Results Parts Graph and Button Panel Description The Graph panel contains a graph of either the average vectors of all of the clusters or of all of the cluster rows along with the cluster average vector depending on whether the AII Clusters button is selected or a specific cluster button is selected Along the x axis the column number is represented which corresponds with the column order as displayed in the heatmap in the lower panel Along the y axis the value is represented Graph All Clusters Value Plot Columns K Means Graph All Clust
121. this button will launch the saved result 77 GenePilot V 1 07b August 28 2003 SAM Graphs Results Parts FDR Graph FDR Plot F Db I R b B 5b D X Daa SAM FDR Graph Description The FDR graph plots the FDR in the y axis against the percentage of the Dataset in the x axis A vertical red line indicates the percentage of rows and FDR for the current Delta selection The shape of the graph can quickly indicate the quality and distribution of data in a Dataset or Run A line that starts out closer to horizontal then curves up indicates a large number of rows that correlate well with the vector A line that starts out with a steep upward curve on the other hand indicates few if any rows that correlate with the vector Actions 1 Clicking along the line will change the Delta value to the closest delta value to the point selected Results Parts Score Graph Expected Store SAM Score Graph Score vs Expected Score Current Delta is plotted in Blue Description The Score Graph plots the score in the y axis against the expected score as calculated through regression in the x axis Ared parallelogram indicates the boundaries of the current Delta Selection Points above the boundaries are red to indicate correlated significance Points below the boundaries are green to indicate anti correlated significance Actions None 78 GenePilot V 1 07b August 28 2003 SAM Heatmap Panel Results Parts
122. ton closes the window without doing the copy IE eel HIBENEE B Te File Pathe Interface Copy to File Diem mapit se COH BM OUpM PUR Description DE EINE This Interface allows the user to select specify a File Path in which 5 ieia C M Reet to write out information contained in this result This information will SeetPaerintormation Fields to inckuda include the rows specified and the Row Information Fieldsthatare I eese chosen Leiden gmba 7 LaeusLink it Select File Path Daiena Marne This selection is used to set the path to the output file Click onthe Summar Fenenen Set Output Path to set the file Traditional copy and paste ane Orikkogransisioas methods work in this field Raprwsertitrve rRNA ace V Rapessareutvo Prot Acc deiiene Conard i Copy to File Interface 74 GenePilot V 1 07b August 28 2003 SOM Search Interface Select how much data to copy This section determines which rows will be selected When All Rows is selected then all of the rows in the current node are copied to the file or all nodes along with their rows are copied if no node is selected When Selected Rows is selected Ifrows are selected in the Heatmap only those rows will be included If anode is selected but no rows are selected all rows in that node will be included If no node is selected then all nodes along with their rows will be copied Select Row Information Fields to include This section allows t
123. tor char This selection sets the character that will separate the information from each field Row Info Field Selection Panel Select Row Info Fields This section allows for selection of the specific fields that will be displayed in the row info and the order of these fields It has the following buttons gt gt This button moves the currently hilited field in the left column over to the right column This button moves the currently hilited field in the right column over to the left column up This button moves the currently hilited field in the right column up one row down This button moves the currently hilited field in the right column down one row 85 GenePilot V 1 07b August 28 2003 SAM Gene Ontology Preferences Button Make Changes This button must be clicked in order for the changes to be made Button Cancel This button cancels any changes that were made and closes the window Preferences Gene Ontology CO ae Cana Ontelegy Settings Panal Descripsan Sanct Bumbar of Gore Ontolog Column a aier I This interface is used to set the Gene Ontology me al End preferences for this screen The choices include apse cg automatic selection of the most common Gene Sewcicwanr S ataca aso Ciar C Uar Select Ontology categories based upon either the currently z Us Shaw Chies List Order Cheices selected rows or for all rows in the current delta range eed caer ae If the selected rows ha
124. ue for SD Mean With a maximum cut off value as a secondary sort 19 GenePilot V 1 07b August 28 2003 Base Interface Replicate Column Combine Button Create Combined Dataset This button executes the creation of the new Dataset with the combined rows 20 GenePilot V 1 07b August 28 2003 Chapter 3 Dataset Display Description The Dataset Display provides a means to view a Dataset prior to running analytics on it It can display all rows only filtered rows or the rows that remain after filtering If one or more Classification Vectors are loaded the rows are sorted by classification 21 GenePilot V 1 07b August 28 2003 Dataset Display Heatmap Panel Parts Heatmap Panel m Ens mim Mhielenoma ERI ed Paste HEB OSES Lung Cancer SSSS0aeg glbsas oH 2 433 a E Colon Forint rowOr a nacOizg Suma psee mo ee to REL ERESSE here ee eee oe 2ee28 8 e Renal E S in es es ESTs 5 3 M0008 m Homo sapiens thrombospondin 3 THBE3 om ROZ GROZ oncogene Chr E0971 Dh clone pjS s b 470934 6 Ae0s44 ESTs Weakhsimilarto HYPOTHETICAL AHSS RESI WI Chr10 276534 rn 2 EN Human microfibril associated glycoprotein EE IL1B Interleukin 1 beta Chrz B24555 D 5 A AD 3 17735 SAAS Sey m m l Human mRNA for IL AOO S7 gene compl Dataset Display Heatmap 1 Heatmap 2 Column Information 3 Class Indication when avail 4 Gene Ontology Names when avail 5 Gene Ontology Indication when
125. umn 2 Vector Type Must begin with Shape Column 3 Vector Name Defines the name of the vector used throughout GenePilot Column 5 leave blank Column 5 to n Column Value Each column must have a number entry Input Vectors Pair Data Optional This entry defines the Pair Data associated with this Dataset This type of vector defines the pairing in Datasets that contain pairs of data Each pair of columns will have it s own pair of numbers starting with 1 1 with one of the pair having a positive value and the other having a negative value Values must start with 1 1 and progress up with no missing gaps You can define and include as many different Pair vectors as you wish All Vectors must be in the rows immediately following the Column Names row The following describes the entries needed Column 1 leave blank Column 2 Vector Type Must begin with Pair Column 3 Vector Name Defines the name of the vector used throughout GenePilot Column 4 lt leave blank Column 5 to n Column Value Each column must have a matching column whose value is matched and opposite Input Data Header Required This entry is used to define the start of the Data portion of the input form It contains the headers that can be used as a column guide The first column must begin with Name of first Row Information Field gt 10 GenePilot V 1 07b August 28 2003 Getting Started Prepari
126. user define criteria for creating a new Dataset from rows of the current Dataset For K Means Clustering one or more clusters can be selected with their rows to be used as the rows for the new Dataset or to be excluded from the new Dataset Note Rows that have been filtered out will be excluded from any new Dataset created this way Quit File gt Quit This selection closes the Result Window 54 GenePilot V 1 07b August 28 2003 K Means Clustering Menu Choices Save Results File gt Save Results This selection is used to save the current result This will save the results of an Analytic run so that the results can be viewed immediately Once an analytic result is saved for a Dataset a button will be added to the Dataset Information screen to quickly view the saved result Search Action gt Search This selection launches the search interface which allows the user to search the rows for a String See Search Interface for more information on the Search Interface For K Means Clustering the search will search the currently selected cluster first it will then continue the search through the remaining clusters then start over at the beginning cluster Search Again Action gt Search Again This selection searches for the next case of the search string using the settings from the last search Select Classification Vector If Avail Classes gt Class Vector Name If there is one or more Classification Vectors then one of thos
127. uses is to only store a percentage of the closest distances This is more complicated in the traditional method but it runs faster and uses far less memory than the traditional method There are 3 choices small medium large with larger clusters For most uses the Small memory model should be sufficient The smallest using less memory and running faster The Largest uses more memory and results in Results Parts Left Panel sill Left Panel Parts 1 Heatmap 2 Column Dendigram 3 Row Dendigram Description This panel displays a small cel version of the heatmap with a row dendigram on the left and a column dendigram above the heatmap when the columns have been clustered The top dendigram is color coded if Classification Vector s are available Clusters can be selected by either clicking on a node in the left dendigram or selecting rows in the heatmap Selecting these clusters will cause the associated rows to be displayed in the right panel 37 GenePilot V 1 07b August 28 2003 Hierarchical Clustering Results Right Panel Heatmap Center The heatmap contains rectangles color coded in the Palette colors to represent the value of each cel juncture of 1 row and 1 column By default these colors are Red highest value and Green lowest value When No Normalize is selected the value range is defined by the min and max values in the entire Dataset Rows remaining after filtering with zero being the medium value Wh
128. ve preference and there aren t Gene Oriciogy Hare E uio enough categories to fill the number of columns then T itegeal is plasma memerase 4 the most common categories across all rows in the sai rections T iniraceliclar S paci 12 delta range are used to fill in the categories Specific Gene Ontology categories can also be specified this is aided by the List Show Choices and List Order Choices for quickly finding specific Gene Ontologies Select Number of Gene Ontology Columns to Euis Top Unseioct as show Sew Changes Canet ve This selection sets the number of columns that will be Gene Ontology Settings Panel displayed Select GO Types in Display This selection sets the Gene Ontology Categories to Display with the following options Biological Process Shows only Biological Process Cellular Component Shows only Cellular Component Biological Process amp Cellular Component Shows both Categories Molecular Function Shows only Molecular Function Biological Process amp Molecular Function Shows both Categories Cellular Component amp Molecular Function Shows both Categories All Shows all three Categories 86 GenePilot V 1 07b August 28 2003 SAM Gene Ontology Preferences Select control for Gene Ontology Columns This selection sets the way that Gene Ontology Columns are selected with the following options Auto Selection Chooses most common Gene Ontologies among selected rows if avail then fills in rema
129. very useful for sending the results of a Dataset analysis to a colleague Upon importing this archive another user can view exactly the same results as the sender Close Dataset File gt Close Dataset gt Dataset Name This selection is used to close an open Dataset If the Dataset being closed is the current Dataset and another Dataset is open then the other Dataset will become the current Dataset Export Dataset File gt Dataset gt Export Dataset This Selection is used to export the current dataset out to the same format that is used for loading a Dataset into GenePilot This can be very useful when a new dataset is created out of a result window Load Dataset Archive File gt Dataset gt Load Archive This is used to load in a Dataset that was Archived with Create Archive Archive Dataset This will include the Dataset information run settings and Saved Results Make Template File gt Dataset gt Make Template This is used to create a template for importing Data This is likely the very first step that a new user will do as itis the necessary first step in bringing data into GenePilot New Dataset File gt New This is used to load a new Dataset into GenePilot The dataset file should be in the format described in Import Format is needs to be in ASCII format with columns of information separated by a Tab Once GenePilot has imported the Dataset the main window will display the Dataset Info screen Open Dataset Fi
130. vised Analysis i e SAM The Classification vectors are used by all the tools to indicate classes i e Breast Cancer Lung Cancer Melanoma etc which is extremely useful when viewing the results Input Name lt Required gt This entry will be the Name that this Dataset is referred to throughout GenePilot It must be located in the second column of the fist row and the first column must have Dataset Name Input Type of Data 0 Other 1 cDNA 2 Affy lt Required gt 8 GenePilot V 1 07b August 28 2003 Getting Started Preparing Data This entry tells the program what type of chip was used to produce the data It can be one of three possibilities 0 Other Data This applies to all data that isn t defined 1 cDNA Data This applies to data created with cDNA style chips 2 Affy Data This applies to data created with Affymetrics chips The number that defines the chiptype for the current Dataset must be located in the second column the first column must have at the start Type of Data Input Model Number lt Optional gt This entry tells the program the model number of the chip if applicable In future releases this information can be used to import additional data about the rows of information such as accession numbers and gene names The model number must be located in the second column with the first column starting with Model Number Input Lead Col Count lt Required Do Not
131. x either manually or using the Select Top button under the list 72 GenePilot V 1 07b August 28 2003 SOM Gene Ontology Preferences List Show Choices This selection sets the Gene Ontologies that will be displayed in the list for selection It has the following choices Show All GO Displays all of the Gene Ontologies that are associated with the current Dataset Show only GO from Node Displays the Gene Ontologies that are associated with genes from the current node Show only GO from Selected Displays only the Gene Ontologies that are associated with the currently selected genes List Order Choices This selection sets the order that the Gene Ontologies are displayed in the list for selection It has the following choices Sort by name Sorts the Gene Ontologies by their name Sort by Node qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently node Sort by Selected qty Sorts by the number of times that each Gene Ontology is associated to a gene in the currently selected genes Button Select Top This button selects the Gene Ontologies that are at the top of the list in the quantity specified Button Unselect All This button unselects all of the currently selected Gene Ontologies Button Save Changes This button sets the currently selected settings and closes the window Button Cancel This button closes the window without setting any of the changes made 73 GenePi
132. y SeleciFisidinbe usedir Gon Ey contains one of the fields that can be used for the S query MEE i Laer Sabes Page Step 1 Select ID Field In this section the Row Info Field that will be Trost of aama In Dane aol Bande used for the query needs to be selected ors ee sat ute ipea NN One Aline UreCans Nac Serre f yat bya Step 2 Save Query File Gane Ontology Annctations Representative mRHA An Fiepreseniabes Peoinin Acc In this section the query file is exported to the e Ghick Sow aii Chester Ie Min railgie C ar File Path that is selected O veraio existing infomation leor Hew informations Canai Step 3 Launch Browser with Submittal Page In this section GenePilot launches a browser window with the URL set to the batch query Row Info Import Interface submittal The File that was saved in Step 2 must be specified then the types of data that are desired must be selected After the Batch is done running the Download the results file link needs to be selected and the resulting web page saved Step 4 Import new information In this section the new Row Information is imported Note that if a Dataset has been reloaded into GenePilot and the first three steps have already been taken and a result page is still present then the second and third steps can be skipped The Field used in the earlier query must be selected and the earlier file can be imported If the Overwri

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