JCONTEXTEXPLORER USER MANUAL
Contents
1. 451 Health Sciences Drive Davis CA 95616 CHAPTER 4 ADDITIONAL RESOURCES 43 TUTORIAL I DETERMINING HPXW FROM GGT IN 22 ALPHA AND GAMMA PROTEOBACTERIA In this tutorial we will recapitulate the analysis described in the JContextExplorer manuscript 1 Retrieve Information Please download the associated biological information for 22 alpha and gamma proteobacteria from the Facciotti lab website http www bme ucdavis edu facciotti resources data software Please click the hyperlink entitled AlphaAndGammaProteobacteria and extract the contents of the directory The resulting extracted directory should contain 1 a file titled HomologyCluster txt 2 a directory titled Annotations and 3 a file titled AlohaAndGammaProteobacteria nwk 2 Load JContextExplorer with tutorial dataset A Either by downloading the zipped JContextExplorer directory and launching locally or using the Java WebStart on the Facciotti Lab Website launch JContextExplorer B Select the newly downloaded extract AlphaAndGammaProteobacteria Annotations directory for genomic working set C When the intermediate GFF checking frame appears click the Proceed to GFF Import with these type processing settings button D Once this has finished loading load the homology clusters in the newly extracted directory AlphaAndGammaProteobacteria HomologyClusters txt E Once this has loaded click the submit button which should launc2. XAND Y IX OR Y 3 Moving Distances In microbial genomes co transcribed features are often grouped into same stranded positionally adjacent groupings operons with little intergenic spacing between them As the spacing between individual features widens this could indicate a change in the transcriptional processing of a genomic grouping for example a large widening in the center of a tightly packed gene grouping could indicate the splitting of one operon into two Also relevant to this comparison is a rearrangement of genes within a single operon gene order in operons may convey information about the relative importance of transcribed products This pairwise comparison metric attempts to capture these behaviors through a weighted sum of observed differences penalties between two genomic groupings X and Y The Moving Distances approach is designed to compare genomic groupings that contain the same set of homologous genes If there is even one inclusion exclusion the two groupings with score a dissimilarity value of 1 maximum dissimilarity Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 Provided that for every gene in gene grouping X there exists a homologous gene in gene grouping Y inversions gene rearrangements between the groupings are assessed A single rearrangement incurs a dissimilarity penalty of 0 2 If rearrangements have occurred the rearrangements are counted and a dissimilarity me
3. Maximum val o7 EEE EE V Show labels Font Color Dissimilarity metric Common Genes Dice EZ Acetobacter pasteurianus IO 3283 01 1 Acidithiobacillus ferrooxidans ATCC 539931 Parvularcula bermudensis HTCC 2503 1 Gluconacetobacter diazotrophicus PAIS I Gluconobacter oxydans 621H 1 Cellvibrio japonicus Uedal07 1 Tolumonas_avensis_DSM_9187 1 Xanthomonas campestris ATCC_33913 1 Dickeya_dadantii_3937 1 Dickeya_zeae_Ech1591 1 Pectobacterium_wasabiae_WPP163 1 Yersinia_enterocolitica_subsp_palearctica_Y 1 1 Erwinia_bilingiae_Eb661 1 Erwinia_pyrifoliae_Ep196 1 Pantoea_ananatis LMG 20103 1 Serratia_proteamaculans_568 1 Klebsiella_oxytoca_MSal l Klebsiella pneumoniae NTUH K2044 1 Klebsiella var cola At22 1 Pantoea_vagans_C9 1 1 Marinomonas sp MWYLI I Teredinibacter turnerae T7901 1 Genomic Segment Viewer Tool Select Nodes Select All y Deselect All 3f View Contexts d View Annotations This is the main window From this window you may 1 build context trees by querying your genomic working set and build context trees 2 edit tree display and construction settings 3 select one or more nodes in a currently active context tree frame or 4 Launch the view annotations and or multi genome browser context viewer window s F
4. Health Sciences Drive Davis CA 95616 27 banner You may remove sets by selecting them from this same drop down list and clicking the Remove button Once you have finished adding removing managing context sets click the OK button to close this frame You may also close this frame by clicking the close box in the upper left or right hand corner of the frame depending on your computer s operating system Available Context Set Genomic Grouping Types 1 Group genes based on intergenic distance Annotated features are organized into non overlapping groups based on 1 intergenic distance and 2 strandedness An intergenic distance threshold field allows the user to specify a cutoff point for grouping annotated features into the same genomic grouping In other words the end of one annotated feature must be no further away from the start of the next annotated feature for these annotated features to be grouped into the same genomic grouping If the Genes must be on same strand checkbox is checked then genes must also be on the same strand This genomic grouping method is often used when organizing the genes on microbial genomes into operons Push the Compute button to sort all annotated features in all genomes in the genomic working set into the appropriate genomic groupings Once this computation is finished a progress bar will appear you may push the add button to load this context set into your set of available context set
5. Homology Clusters Input Instructions Within a single genomic working set certain annotated features may be homologous to one another This may occur both within a single species and across multiple species A group of homologous features is often referred to as a Homologous Gene Cluster or simply a Homology Cluster Numerous methods exist to detect homology across and within genomes and to cluster annotated features in a set of genomes into homology cluster groups Often but not necessarily these homology cluster groups are non overlapping That is each annotated feature may belong to a maximum of one homology cluster For all homology cluster associated processes JContextExplorer assumes non overlapping homology clusters When JContextExplorer searches for annotated features in a genomic working set it may do so either by 1 Matching a textual query to individual genomic feature annotations or 2 Matching a homology cluster ID number Textual annotations may be unreliable especially if a genomic working set contains genomes annotated by different groups so it may be worthwhile to compute homology clusters and load these computed homology clusters into JContextExplorer WARNING JContextExplorer cannot compute homology clusters from a set of sequenced genomes only search a set of pre computed loaded homology clusters To load a set of pre computed homology clusters click the load button below the banner and select the ap
6. Joint Between Within E Precision EE Returning to the main frame in the upper left hand corner in the Search Genomes sub panel you should see two radio buttons one titled Annotation Search and the other titled Cluster Number Make sure Cluster Number is selected 1 In the text field below type the number 150 2 Below this you should see the banner titled Context Set From the drop down menu select the newly created context set D75 3 Directly below this panel you should see another panel titled Display Settings In the drop down menu associated with Dissimilarity Metric select Common Genes Dice 4 Directly below in the drop down menu associated with Clustering Algorithm select Joint Between Within 5 Finally return to the Search Genomes sub panel and push the Submit Search button 6 Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 46 5 Select portion of Tree for Context Viewing The following 5 steps are displayed and described below rsion 1 0 Cluster 150 D75 Serratia proteamaculans 568 2 Teredinibacter turnerae T7901 2 Teredinibacter turnerae T7901 3 Xanthomonas campestris ATCC JOA Yersinia enterocolitica subsp palearctica Y 11 1 Acetobacter pasteurianus EO 3283 01 2 Gluconobacter_oxydans_621H 3 Erwinia pyrifoliae Ep196 3 Gluconobacter_oxydans_621H 2 Gluconobacter_oxydans_621H4 Parvularcula_bermudensis HTCC_2503 1 Xanthom
7. Sciences Drive Davis CA 95616 4 3 Discovering and interpreting potential horizontal gene transfer events 4 Within a set of duplicated homologous genes across species determining which copies are ancestral and which represent more recent expansions Within the umbrella of genome exploration JContextExplorer s GUI interface allows one to 1 Peruse annotated features nearby to a gene or genes of interest 2 Compare and count textual annotations within a set of homology clusters 3 Effectively merge one or more context sets into superclusters These are but a short list of suggested uses Any comparative genomic analysis that could benefit by alternative methods of organization and visualization of multiple genomes or section of multiple genomes stands to benefit from JContextExplorer For a few examples of some biologically interesting uses please see Chapter 4 Additional resources Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 CHAPTER 2 LAUNCHING JCONTEXTEXPLORER WHERE I CAN FIND JCONTEXTEXPLORER JContextExplorer can be found on the software Facciotti lab website http www bme ucdavis edu facciotti resources data software On this website JContextExplorer is available both 1 as a Java WebStart and 2 as a downloadable zipped directory Supplementary documentation instructions and links to video tutorials may also be found on this page JContextExplorer is distributed
8. a grouping of genes that exist on the same genome These groupings are the elements that form the leaves of all generated context trees A context set describes how genomic neighborhoods should be defined There are many ways to describe context sets As a default JContextExplorer will create a context set called SingleGene which consists only of the annotated feature that matches the search query You may add remove and manage context sets by clicking the Add Remove button below the Select Context Set banner shown above A detailed description of available ways to define context sets is available in the Add Remove Context Sets section page XXX Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 21 Editing Tree Display and Construction Settings Update Tree Display Settings Dissimilarity metric Common Genes Dice EE Clustering algor Unweighted Average E H4 Precision EO V showaxis Color EA CAMERE Color Minimum value 0 Maximum value 0 7 Ticks separation 0 1 Nodes size 6 Hd V showiabas Font Color V showlabds Font Color a Labels every 1 ticks Labels orientat Horizontal Hd Context Trees may be edited in various ways following their computation both in terms of 1 their construction and 2 their display The majority of features in this tool were previously developed in the Multidendrograms software packag
9. contain an annotated feature to make this frame disappear left click on a different annotated feature to display biological information for that annotated feature 39 Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 Right Clicking Save contexts as JPG Save contexts as PNG f Save contexts as EPS Show Legend Complete Show Legend Clusters Right clicking anywhere on the frame opens the pop up menu displayed above left clicking away causes this popup menu to disappear Selecting any of the image export options will open a file dialog allowing for image export In the image export only the rendered genomic contexts will appear and they will always appear exactly as they do on screen Selecting any of the Show Legend options will launch the Gene Color Legend frame please see Gene Color Legend page XXX Middle Clicking Middle clicking on a particular annotated feature will select all other annotated features with the same homology cluster or annotation depending on the initial search type You may hold down the CTRL or SHIFT key while middle clicking which will allow for selection of multiple annotated feature groups If you have the Gene Color Legend frame open then the entry associated with this annotated feature will also appear selected surrounded by a thin red rectangle Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 41 GENE COLOR LEGEND eno Gene Color Le
10. group ID or common annotation just as the genomic groupings are colored If Show Surrounding is unchecked this option has no effect If Strand Normalize is checked individual genomic segments may be displayed in sequence reverse complement so that query matches are on the forward strand If the genomic segment is already oriented such that query matches are displayed on the forward strand this option has no effect Range to Display Before 1000 nt After 1000 nt Update Contexts This is the Range to Display sub pane This controls how much of the surrounding genomic region should be displayed along with individual genomic groupings Changing values in the Before and After text fields and clicking the Update Contexts text field will re render all genomic segments in the range to display sub pane The Update Contexts button is also linked to the leaves selected on the associated Context Tree for the rendered contexts You may change the Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 rendered contexts by changing the leaves selected in the context tree frame and pushing the Update Contexts button Left Clicking Cr This is the gene information sub frame Left clicking on an individual annotated feature results in a small yellow box appearing at the point of clicking displaying biological information about the annotated feature clicked Left click on another part of the frame that does not
11. 16 ADD REMOVE CONTEXT SETS GOO Add or Remove Context Sets ADD A CONTEXT SET Enter Name Sample Group genes based on intergenic distance f Compute V Genes must be on same strand e Group genes based on nucleotide range nt Before 1000 nt After 1000 O Group genes based on number of nearby genes Genes Before 2 G Group all genes between two queries together Group multiple independent queries together Load gene groupings from file Load Create a new context set by combining existing context sets Launch Context Set Combiner Too All genes within a defined range of a single gene query are grouped together Context Set SingleGene EZ Remove O N A y OK pn This is the add remove context sets frame From this frame you may define new genomic grouping protocols or remove unwanted existing genomic grouping protocols To add a new genomic grouping protocol first type a name for your new genomic grouping in the Enter Name text field Then select the appropriate scheme for genomic grouping computation all available schemes described below Once your set is ready to add you will see a message appear in the text field next to the add button Click the add button to add this to the set of existing genomic grouping methods This new method will appear in the drop down list of existing context set definitions under the Remove a context set Facciotti Lab UC Davis 451
12. 2 Annotated feature start position column 3 Annotated feature stop position column 4 Context set ID Number Please format files carefully prior to import into JContextExplorer 7 Create a new context set by combining existing context sets This feature has not yet been implemented yet When implemented it will attempt to allow integration combination of multiple alternative context set creation schemes into a single method Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 30 VIEW ANNOTATIONS eno Annotation Results Annotations for 17 selected nodes Haloarcula argentinensis 1 EC number 3 5 3 11 db_xref GO 0008783 product Agr Haloarcula californiae 1 EC number 3 5 3 11 db_xref GO 0008783 product Agmatir Haloarcula japonica 1 EC number 3 5 3 11 db_xref GO 0008783 product Agmatina Haloarcula marismortui 1 EC number 3 5 3 11 db_xref GO 0008783 product Agma Haloarcula sinaiiensis 1 EC number 3 5 3 11 db_xref GO 0008783 product Agmatir Haloarcula vallismortis 1 EC number 3 5 3 11 db xref GO 0008783 product Agmat Halobiforma nitratireducens 1 EC number 3 5 3 11 db xref2GO 0008783 product Halococcus saccharolyticus 1 EC number 3 5 3 11 db xref GO 0008783 product Ac Halococcus salifodinae 1 EC number 3 5 3 11 db xref GO 0008783 product Agmati Haloferax denitrificans 1 EC number 3 5 3 11 db xref GO 0008783 product Agmat Haloferax elongans 1 EC number 3 5 3 11 db xref GO 0008783 product Ag
13. 30 0 20 0 10 0 00 Halalkalicoccus jeotgali B3 DSM 18796 1 Halococcus hamelinensis 1 Haloferax sp GUBF 3 1 This is an example of a Context Tree frame These frames appear as internal frames to the JContextExplorer main frame Upon performing a search using JContextExplorer will appear in a new Context Tree frame as a generated context tree As a reminder the context tree displayed in the frame is a function of the 1 search query 2 context set 3 pairwise dissimilarity metric and 4 clustering or linkage method The display and computation of the tree may be re determined with a new context set Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 32 dissimilarity metric or clustering method by changing all parameters appropriately and clicking the Update Tree button in the main frame Alternatively changing parameters and clicking the Submit button in the main frame retains the old context tree and creates a new context tree using the updated parameters Multiple context tree frames may be managed simultaneously they may be moved re sized minimized maximized closed and restored Multiple investigations may occur simultaneously through minimizing and restoring individual context tree frames Tree frames are interactive both by 1 Left Click and 2 Right Click Left clicking on a frame selects leaves for annotation context viewing while Right clicking launches a pop up menu show
14. JCONTEXTEXPLORER USER MANUAL Phillip Seitzer Lc cs peg FACCIOTTI LAB A d UC DAVIS November 2012 Version 1 07 TABLE OF CONTENTS CHAPTER 1 GETTING START ED ui oio ae rua eo ao aa EE ak e ne cona azkan at Eate 3 bLvdci es nasi Cleriico M 3 WHY SHOULD USE JCONTEXTEXPLORER sas aea 4 CHAPTER 2 LAUNCHING JCONTEXTEXPLORER 44 eee eee no sen 6 WHERE I CAN FIND JCONTEXTEXPLORER cesse eese eee aea 7 WHAT DO NEED TO DO BEFORE CAN LAUNCH JCONTEXTEXPLORER eese eee 7 CHAPTER 3 USING JCONTEXTEXPLORER ee eee eee nenne nenne eae aaa 8 SUMMARY OF available FEATURES rrura 9 GORE WINGOW e 10 Genomic Working Set Input Instructions aa 11 GFF File Type Import SERE Errarte rera a adareta raga 13 Homology Cluster Input ISTU OE rra 15 M in Frame nnn 18 Searching a Genomic Working Set rra 20 Editing Tree Display and Construction EGUES sas 21 Available Pairwise Dissimilarity Metrics rraza 21 Launching Subordinate Windows and Selecting Nodes ra 25 Add Remove Context EGZ 26 Available Context Set Genomic Grouping TERE rra 27 VIC W else iseiioje svi a a eai ea E sae araka rare 30 Context Tree Frame see tc EE EE ea EE teca susie ten tument T etd e Ene E du eeu cud ee reed neas 31 Baul e gele 33 Right Click ela 34 Multi Genome browser Context Viewer wicccccccccccccccccccc
15. acciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 19 Searching a Genomic Working Set eoo Gene Context Search Annotation Search 9 Cluster Number 2 Submit Search Context Set Operons B Add Remove N 5 Type your search in the search bar shown above If you select the Annotation Search radio button JContextExplorer will search through the associated feature annotation for exact case insensitive matches All genomic groupings that contain one or more annotated features that match the textual query are retrieved compared and assembled into a context tree If instead you select the Cluster Number radio button JContextExplorer will search through associated loaded homology cluster ID numbers for an exact match If you would like to specify multiple queries the equivalent of an OR statement separate your search queries using a semicolon For example a search of 3 with the cluster number radio button selected will search for all annotated features with a cluster ID number of 3 a search of 3 51 will return all annotated features with a cluster ID number of 3 OR 51 Under the banner Select Context Set there is a drop down menu allowing you to choose which context set you would like to use for your search A Context Set is Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 20 a set of genomic groupings A genomic grouping is simply
16. are each object to be clustered with each other object to be clustered and 3 assemble these comparisons into a tree link individual dissimilarities using standard clustering approaches JContextExplorer also allows for fast searching a set of annotated genomes as well as several flexible visualization tools As evident in the name JContextExplorer is designed to facilitate exploration Each of the three major steps in context tree creation genomic grouping definition pairwise comparisons tree creation may be re computed quickly and easily with alternative parameters The graphical interface is designed for point and click investigation and provides fast and easy export of major results context trees multi genome context renderings etc We strongly suggest using the automated features tree computation in concert with the manual interrogation features multi genome browser in your investigations WHY SHOULD I USE JCONTEXTEXPLORER There are many reasons to use JContextExplorer These reasons tend to fall into two categories 1 Reasons relating to genomic context or gene neighborhood comparison and 2 reasons relating to annotated feature exploration Within the umbrella of genomic context comparison one might be interested in 1 Resolving ambiguities in annotated features 2 Comparing changes in gene regulatory network structure as in the case of operons in microbial species Facciotti Lab UC Davis 451 Health
17. as an executable JAR However it is also possible to build the tool from source All source code is available on GitHub https github com PMsSeitzer JContextExplorer WHAT DO I NEED TO DO BEFORE I CAN LAUNCH JCONTEXTEXPLORER JContextExplorer runs on the Java Virtual Machine JVM version 1 6 or higher If you do not have the Java runtime environment installed please install the latest version of Java before attempting to launch JContextExplorer The Java Webstart version runs with a maximum heap size of 512 MB Please make sure your system can accommodate for this memory allocation if not please use the zipped directory version instead of the WebStart version If you are using the WebStart version to launch JContextExplorer simply click the WebStart launch button If you have downloaded a JContextExplorer in the zipped directory you may either A double click on the icon or B launch JContextExplorer from the command line with the following command java jar lt path to file gt JContextExplorer jar You may want to launch java with a larger max heap size to avoid memory related problems In that case type the following command java Xmx256M jar path to file JContextExplorer jar Of java Xmx512M jar lt path to file gt JContextExplorer jar CHAPTER 3 USING JCONTEXTEXPLORER SUMMARY OF AVAILABLE FEATURES JContextExplorer is organized as a series of major and minor windows laid out in a semi hierar
18. asure is returned Therefore if 5 or more rearrangements are counted genomic groupings are returned with a dissimilarity score of 1 maximum dissimilarity If no rearrangements have occurred distance widening based penalties are then assessed If no widening has occurred between analogous genes across genomic groupings no penalty is incurred If a slight widening between 10 and 25 nt has occurred this incurs a dissimilarity penalty of 0 02 If a medium widening has occurred between 25 and 200 nt has occurred this incurs a dissimilarity penalty of 0 05 If a large widening has occurred greater than 200 nt has occurred this incurs a dissimilarity penalty of 0 2 Note that this widening often signifies a gene insertion In future versions of this software more user control will be allowed to modify the various penalties assessed and the values to associated with these penalties The set of penalties penalty values included here are designed to be effective for comparing highly phylogenetically similar organisms within the same phylum or else highly conservative genomic groupings d SUM penalties 4 Total Length The total size of each genomic grouping X and Y is computed by taking the distance from the start of the earliest annotated feature to the stop of the Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 24 latest annotated feature The dissimilarity is taken to be the average differ
19. ccccecececuescueueueussecscscssecececececececeseeseceueeeseuacusacauaaaea 36 Gene Information sub pane ss 37 Genome Display GURAGO 37 HETARA EUA D E EAEE 38 Lefteclick ALA 39 Right click optioris seii dites e een na feit l a rad E esi ni Da Iesu D edi va dite sa ees YE Ee dr REN 40 Middle click options sa 40 GENE Color Legend A 41 CHAPTER 4 ADDITIONAL RESOURCES ccscccsscssscnccessccsscnsccnscssscnsccnsccnscnssenscesssecscnsseeseassonesens 42 TUTORIAL I DETERMINING HPXW FROM GGT IN 22 ALPHA AND GAMMA PROTEOBACTERIA eese eene 43 TUTORIAL 2 COMPARING A JCONTEXTEXPLORER GENERATED CONTEXT TREE TO A PHYLOGENETIC TREE 47 VIDEO TUTORIALS e aai 49 AUTHOR CONTACT INFORMATION ccccssccesseccnceccceccccesesccseccesccceeescoeceecnsecueeseoeceecesesaceesoussccuesssoucesesseouens 51 Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 2 CHAPTER 1 GETTING STARTED WHAT IS JCONTEXTEXPLORER JContextExplorer is a tool to facilitate cross species genomic context comparisons based on previously determined annotated genomes and possibly homology clusters JContextExplorer uses variable group agglomerative hierarchical clustering to create context trees where each leaf represents a single gene neighborhood JContextExplorer offers several ways to 1 define genomic groupings i e create the objects to be clustered 2 perform pairwise comparisons comp
20. chical manner Main Window Annotations Add Remove Color Legend Gene Context Sets Information From an initial starting frame a main window is launched This main window has several child windows including the Context Viewer or multi genome browser window which also has several child windows Please see the instructions associated with each window for more information START WINDOW e neo Welcome to JContextExplorer Genomic Working Set required Load No file currently loaded Homology Clusters optional Load No file currently loaded Submit This is the starting window All input files should be entered at this point Input files consist of 1 The Genomic Working Set files directory and 2 Homology Cluster files In each case upon clicking the Load button a file chooser will appear allowing the user to select the appropriate file directory Once appropriate the files directory have been loaded please push the submit button to proceed to the main frame 10 Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 11 Genomic Working Set Input Instructions A Genomic Working Set is a collection of annotated genomes When performing searches in JContextExplorer JContextExplorer will query all genomes in the loaded genomic working set To load a genomic working set push the load button below and either 1 Select a directory c
21. e Gomez S Fernandez A Montiel J amp Torres D n d Solving Non Uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms Journal of Classification 65 43 65 doi 10 1007 s00357 008 A complete user manual is available at http deim urv cat sgomez multidendrograms php description Please refer to this documentation for more information Available Pairwise Dissimilarity Metrics A feature that exists in this tool that did not exist in the previous multidendrograms package is the various ways to compute pairwise dissimilarities between genomic groupings 1 Common Genes Dice All common genes are identified between two genomic groupings Common genes are defined either by common cluster ID number if the Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 search carried out is homology cluster based or annotation if the search carried out is annotation based The pairwise dissimilarity between gene groupings X and Y is computed according to the Dice Formula d 1 2 XANDY IX IY1 2 Common Genes J accard All common genes are identified between two genomic groupings Common genes are defined either by common cluster ID number if the search carried out is homology cluster based or annotation if the search carried out is annotation based The pairwise dissimilarity between gene groupings X and Y is computed according to the J accard Formula dz1
22. e dendrogram as Newick tree e Haloterrigena_salina 1 Save dendrogram as JPG Save dendrogram as PNG Save dendrogram as EPS Halorubrum litoreum 1 Halorubrum terrestre 1 Natrialba chahannoensis 1 Right clicking anyway on the frame will bring up the pop up menu shown in the figure above These options are borrowed from the original MultiDendrograms software package Gomez S Fernandez A Montiel J amp Torres D n d Solving Non Uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms Journal of Classification 65 43 65 doi 10 1007 s00357 008 Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 35 A complete user manual is available at http deim urv cat sgomez multidendrograms php description Please refer to this documentation for more information Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 MULTI GENOME BROWSER CONTEXT VIEWER eoe Context Viewer Cluster 2 Dickeya dadantii 3937 1 SS Er eee Oe RH Dickeya zeae Ech1591 1 td Pectobacterium_wasabiae_WPP 163 1 9 o A S Yersinia enterocolitica subsp palearctica Y11 1 CBE e Erwinia billingiae Eb661 1 SS a Erwinia pyrifoliae Ep196 1 E d Pantoea ananatis LMG 20103 1 E 0 PH Serratia proteamaculans 568 1 Start M Size M Cl
23. e smallest total distance between annotated features of each type For this context set it is appropriate to push the add button once the radio button is selected 5 Group multiple independent queries together Typically multiple queries are treated as OR statements With this context set however all query matches within a single genome are placed into the same genomic grouping For example a homology cluster search of 15 16 17 will result in grouping all instances of the annotated features with homology cluster numbers 15 16 and 17 into a common gene grouping for each genome searched For this context set it is appropriate to push the add button once the radio button is selected 6 Load gene groupings from file The user may wish to define genomic groupings in one or more organisms using a method not supported by JContextExplorer for example as a result of an experiment They may load these genomic groupings into JContextExplorer by creating a file called a Context Set File a two column Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 tab delimited file which should contain in column 1 the name of the organism and in column 2 the full path to another file an individual context file An individual context file should be created for each organism of interest Each file should be a 4 column tab delimited file with the following information in each column column 1 Sequence name column
24. eld please use underscores instead of spaces 3 Three Column Format Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 If there are 3 tab delimited entries in the line entries take on the following values Column 1 Genome Name Column 2 Annotation Key Column 3 Homology Cluster ID Number This format is identical to Four column format however does not check for agreement in the sequence name 4 Two Column Format If there are 2 tab delimited entries in the line entries take on the following values Column 1 Annotation Key Column 3 Homology Cluster ID Number All features in all genomes in the genomic working set with an annotation that contains the Annotation Key are assigned the provided Homology Cluster ID Number 5 Single Column Format If there is only a single entry in the line this entry is taken to be the Annotation Key All annotated features that contain the annotation key are given a homology cluster ID number which is determined by the line number in the file Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 18 MAIN FRAME Gene Context Search Annotation Search 9 Cluster Number 2 Submit Search ee JContextExplorer version 1 0 Cluster 2 Operons Context Set Operons Add Remove Update Tree Display Settings Clustering algor Unweighted Average Ei showaxis C Color Minimum vah U J
25. ence d 2 ABS IXI IYT IXI IYI Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 25 Launching Subordinate Windows and Selecting Nodes Genomic Segment Viewer Tool Select All i Deselect All Select Nodes View Contexts View Annotations Typing into the text field directly under the Genomic Segment Viewer Tool banner allows for selection of appropriate leaves in the active context tree frame All nodes that contain the search text will be selected To select nodes type your query and push the Select Nodes button or strike the enter key Please note that you may also select leaves by clicking directly on the leaf name as explained in the Context Tree Frame section page XXX If you would like to specify multiple queries the equivalent of an OR statement separate your search queries using a semicolon or white space For example if you would like to select all nodes that contain the text coli or subtilis type coli subtilis or coli subtilis To launch the view annotations frame push the View Annotations button with the appropriate leaves selected This will display the associated annotation of all query matches within the genomic grouping associated with that leaf Similarly you may launch the multi genome browser by pushing the View Contexts button with the appropriate leaves selected Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 956
26. ersion current as of November 17 2012 and perform many of the steps of tutorials 1 and 2 Video 04 Updates November 17 2012 http www youtube com watch v sJNdsGGma 8 amp feature plc Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 50 Video 05 Export a Context Tree http www youtube com watch ev EehARCQ1jTc amp feature plc These two videos are available in a single video playlist http www youtube com watch v sJNdsGGma 8 amp listZPLPCFAX54wfPlvaufZd n7pO799m5klLXw amp feature plcp Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 51 AUTHOR CONTACT INFORMATION The chief author of this manual and software is Phillip Seitzer He can be reached by email at pmseitzer ucdavis edu Phillip Seitzer is a member of the Facciotti lab at the University of California at Davis http www bme ucdavis edu facciotti The source code for JContextExplorer is hosted on GitHub https github com PMSeitzer JContextExplorer Please do not hesitate to contact the author with questions comments bug reports feature requests and more Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616
27. gend Color Cluster ID Annotation none multiple annotations exist 191 PRODUCT UBIQUINONE BIOSYNTHESIS MONOOXYGENASE UBIB MEN 196 PRODUCT NA CA2 EXCHANGING PROTEIN 633 PRODUCT EUKARYOTIC TRANSLATION INITIATION FACTOR 5A 990 PRODUCT FIG 137478 HYPOTHETICAL PROTEIN YBGI Ea 1194 EC_NUMBER 3 5 3 11 DB_XREF GO 0008783 PRODUCT AGMATINASE e E lt gt This is the Gene Color Legend frame It contains the mapping between colors cluster ID and annotations associated with its parent ContextViewer frame The Gene Color Legend is an active frame You may Left Click Middle Click or Right Click If you Left or Middle click you will select the associated color clusterlD annotation relationship in the frame as well as in the parent ContextViewer window Holding down the CTRL key while clicking on a color clusterlD annotation mapping will select that mapping if it unselected or deselect that mapping if it is selected without changing the selection profile of the other mappings Holding down the SHIFT key while clicking on a leaf node will select every mapping between the currently selected mapping and the closest previously selected mapping Selections in this frame will appear in the parent ContextViewer frame If you right click anywhere on the frame you will open a pop up menu allowing for various figure export options as jpg png or eps files Facciotti Lab UC Davis
28. h the JContextExplorer main frame Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 44 3 Define the D75 Context Set A In the upper left hand corner of the main frame below the banner that says Select Context Set click the Add Remove button When you have done so you will see a window that looks like the Add Remove Context Sets window see page 24 B In the text field to the right of Enter Name type D75 C Select the radio button Group genes based on intergenic distance D In the text field directly under this radio button change 20 to 75 Leave the Genes must be on the same strand option checked Then click the compute button next to this field This will take a few seconds to compute E Once it has finished find the Add button of the way down the frame and click this button Note that in the Context Set drop down menu near the bottom of this frame you will now see D75 in the list F Click the OK button at the bottom of the frame Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 45 4 Set appropriate parameters conduct search The following 6 steps are displayed and described below eoo Gene Context Search _ Annotation Search Cluster Number Submit Search Context Set D75 e Add Remove Remove Update Tree Display Settings Dissimilarity metric Common Genes Dice Tr Clustering algor
29. ing several additional available options A red rectangle will appear around Selected leaves Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 33 e no Search Query Cluster s 8000 D50 0 50 0 45 0 40 0 35 0 30 25 0 20 0 15 0 10 0 05 0 00 Halococcus_salifodinae Haloterrigena_salina 1 Halorubrum litoreum 1 Halorubrum terrestre 1 Natrialba chahannoensis 1 Example the 3 nodes on the bottom of this tree are selected while the two nodes on the top are unselected Left Click Options Clicking on an individual leaf node name will select it Clicking on a different leaf node name will de select the previously selected leaf node and select the new leaf node name Holding down the CTRL key while clicking on a leaf node will select that leaf node if it unselected or deselect that leaf node if it is selected without changing the selection profile of the other leaf nodes Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 34 Holding down the SHIFT key while clicking on a leaf node will select every leaf node between the currently selected leaf node and the closest previously selected leaf node Right Click Options eno Search Query Cluster s 8000 D50 0 50 0 45 0 40 0 35 0 30 0 25 0 20 0 15 0 10 0 05 0 00 Show ultrametric deviation measures ee ee Show dendrogram details Save ultrametric matrix as TXT Save dendrogram as TXT Sav
30. matinas Haloferax gibonsii 1 EC number 3 5 3 11 db xref GO 0008783 product Agmatinase Haloferax larsenii 1 EC number 3 5 3 11 db xref GO 0008783 product Agmatinase Haloferax mediterranei 1 EC number 3 5 3 11 db xref GO 0008783 product Agmat Haloferax mucosum 1 EC number 3 5 3 11 db xref GO 0008783 product Agmatina 1 Haloferay nrahovense 1 r 11 dh vxref2GO 0008783 nraduct Aamati oS tt te ee ee 4 gt A Select Nodes This is the View Annotations frame It can be launched from within the main frame please see Launching Subordinate Windows and Selecting Nodes page XXX The annotation frame produces a selectable text window containing the annotation for the query match associated with each leaf in the context tree window The first line always lists the number of nodes selected in this example 17 nodes are selected Following this the node name is given in bold followed by the annotation associated with the query match is given in regular text A search bar exists below which allows the user to type one or more node name queries or textual fragments and select appropriate nodes in the tree This search bar works the same as the node selection bar in the main frame Please see Launching Subordinate Windows and Selecting Nodes page XXX Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 31 CONTEXT TREE FRAME eno Search Query Cluster s 10000 D50 0 70 0 60 0 50 0 40 0
31. mation sub pane These check boxes describe which biological information should be displayed upon left clicking on an individual annotated feature in the ContextViewer frame Genome Display Show Coordinates Show Surrounding v Strand Normalize Color Surrounding This is the Genome Display sub pane These check boxes describe how whole genomic segments should be rendered in the above ContextViewer pane if Show Coordinates is selected numerical values will appear below individual rendered genomic segments displaying coordinates every 1000 nt or so The name of the sequence will also appear in the upper left hand corner and a small triangular flag will appear in the upper left hand corner of each genomic segment Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 38 pointing in increasing order If this flag is black and pointing to the right the sequences are increasing left to right if the flag is red and pointing to the left the sequence is displayed in reverse complement and so is increasing right to left If Show Surrounding is checked annotated features that are not a member of the genomic grouping associated with the genomic segment displayed will also be displayed These features may either be displayed as colored or gray depending whether or not Color Surrounding is checked or unchecked If Color Surrounding is checked annotated features will be colored according to common homology
32. of tRNA This tool allows you to specify how to handle different types of annotated features In general among all possible feature types you may specify 1 The types that should be retained for both genomic grouping computation and display 2 The types that should be excluded from genomic grouping computation but retained for display and 3 The types that should be excluded altogether Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 14 Types in the list Types to Include in Genomic Groupings left will be retained for both genomic grouping computation and display Types in the list Types to Include for Display only right will be retained for display only when viewing genomic segments All other types will be ignored excluded altogether To add types to a list type in the type in the text field below the list and push the Add button To remove types from a list select the type with your mouse and push the Remove button To transfer types from one list to another select the type with your mouse and drag the type to the other list WARNING Features in the GFF file may not overlap in the genomic coordinates they span In the case that they do overlap JContextExplorer will exhibit unpredictable behavior and likely fail Please ensure that no annotated features overlap prior to loading GFF files Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 15
33. onas campestris ATCC 339132 Xanthomonas campestris ATCC AIDA Acidithiobacillus_ferrooxidans_ ATETZ Erwinia_billingiae_Eb661 1 Cellyibrio_japonicus_Uedal07 1 Marinomonas_sp_MWYL1 2 Tolumonas auensis DSM 9187 1 Teredinibacter turnerae T7901 1 Gluconacetobacter diazotrophicus PAIS 1 Parvularcula bermudensis HTCC 2503 2 Dickeya dadantii 3937 1 Dickeya zeae Echl591 1 Erwinia_billingiae_Eb661 3 Klebsiella_oxytoca_MSal 1 Klebsiella pneumoniae NTUH K2044 2 edo Klebsiella_yariicola_At 22 1 Pantoea ananatis LMG 20103 1 Pantoea vagans C9 1 2 Pectobacterium wasabiae WPP163 2 Serratia proteamaculans 568 3 Yersinia enterocolitica subsp palearctica Y 11 2 Erwinia pyrifoliae Ep196 1 ER Select Nodes View Contexts View Annotations JContextExplorer now searches through all genomes for genes in homology cluster 150 returns all associated gene groupings and renders a tree 1 comparing all gene groupings in all organisms containing a gene in homology cluster 150 To view the actual contexts scroll down on the internal child window as far as you can go and right click on the node labeled Cellvibrio japonicus Ueda107 1 2 Hold down the shift key and right click on the node Erwinia pyrifoliae Ep196 1 3 This will select all intermediate nodes 4 Finally click on the View Contexts button 5 This will bring up the multi genome brow
34. ontaining individual annotated genome files or 2 Select a genomic working set file Individual annotated genomes should be formatted in General Feature Format or GFF version 2 a standard tab delimited text file format GFF files should have the file extension gff Each line in the GFF file describes a single annotated feature and is split into 9 columns This program only reads in columns 1 3 4 5 7 and 9 which contain the following information Column 1 Sequence name Column 3 Feature Type Column 4 Feature Start Position Column 5 Feature End Position Column 7 Strand Column 9 Annotation If you specify a directory of GFF files JContextExplorer will name each genome according to the name of the file For example SomeDirectory CollectionOfGenomes Organism1 gff will be named Organism1 Please avoid names containing white spaces instead use underscores Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 12 Instead of specifying a directory of GFF files you may specify a single genomic working set file This file must be a 1 or 2 column tab delimited text file In the first column please specify the file path to all annotated genome files you would like to include in your genomic working set If you do not include a second column each genome will be named according to the name of the file The optional second column consists of a customized name for each genome WARNING When
35. poser package open this file using file open This will launch the phylogenetic tree While this file is loaded in the window open the JContextExplorer generated context tree in the same window again using file open Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 48 4 Explore the features of TreeJuxtaposer TreeJuxtaposer is well documented Please see the documentation page http olduvai sourceforge net tj documentation shtml Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 49 VIDEO TUTORIALS Several video tutorials are publically available on youtube To visit the video page please navigate to http www youtube com user jcontextexplorer feature results main There are currently 5 video tutorials available on this youtube movie channel The first three videos provide a brief introduction to JContextExplorer demonstrate how to retrieve the program and demonstrate using JContextExplorer Video 01 Introduction http www youtube com watch v SJ1wcsnErsg amp feature plc Video 02 Retrieval http www youtube com watch v ZbWAd oXHu4 amp feature plc Video 03 Usage http www youtube com watch vzzlt2qTeVe7o amp feature plc These three videos are available in a single video playlist http www youtube com watch v SJ1wcsnErsg amp listZPLPCFAX5A4wfPnrlPC qZ2gEb9aaQrLSyE6Y amp feature plcp The next two videos highlight recent updates in features showing the v
36. propriate file Homology clusters may be defined according to gene name or precise feature coordinates All files must be tab delimited and each line in the file describes an individual feature homology group relationship Depending on the number of columns provided each line is parsed differently Lines in the file that do not follow the specifications described below will be ignored Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 16 There are 5 acceptable line formats 1 Five Column Format If there are 5 tab delimited entries in the line entries take on the following values Column 1 Genome Name Column 2 Sequence Name Column 3 Feature Start Position Column 4 Feature End Position Column 5 Homology Cluster ID Number If a feature starts at Feature Start Position and stops at Feature Stop Position on the sequence named Sequence Name in the genome named Genome Name this feature is assigned the provided Homology Cluster ID Number 2 Four Column Format If there are 4 tab delimited entries in the line entries take on the following values Column 1 Genome Name Column 2 Sequence Name Column 3 Annotation Key Column 4 Homology Cluster ID Number If a feature contains the string Annotation Key in it s annotation and is found on the sequence named Sequence Name in the genome named Genome Name this feature is assigned the provided Homology Cluster ID Number In the Annotation Key fi
37. s 2 Group genes based on nucleotide range Genomic groupings are determined by including all annotated features that are at least partially contained within the defined range of nucleotides around query matches The range of values around query matches to take may be edited in the nt Before and nt After text fields For this context set itis appropriate to push the add button after specifying values for the number of nucleotides before and after the center of the query match to include in the context set Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 3 Group genes based on number of nearby genes Genomic Groupings are determined by taking some number of annotated features both before and or after all query matches The number of features to include may be edited in the Genes Before and Genes After text fields For this context set it is appropriate to push the add button after specifying values for the number of genes before and after the query match to include in the context set 4 Group all genes between two queries together All annotated features between and including two query matches are included into genomic groupings This genomic grouping requires that exactly two queries be provided Failure to do so will result in an error message In the case that multiple instances of one or more of the individual query types exist in an annotated genome JContextExplorer will use the pairings that result in th
38. ser context viewer window Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 47 TUTORIAL 2 COMPARING A JCONTEXTEXPLORER GENERATED CONTEXT TREE TO A PHYLOGENETIC TREE This tutorial is an extension of the previous tutorial Please perform all steps in tutorial 1 to the point where you have generated a context tree for homology cluster 150 in the D75 context set using the Joint Between Within clustering algorithm and Common Genes Dice Dissimilarity measure 1 Export the context tree With the previously generated context tree in the active window right click anywhere within the context tree frame A pop up menu should appear Select the 5 option from the drop down list save dendrogram as Newick tree Save this tree somewhere on your file system 2 Launch TreeJuxtaposer Open an Internet browser and navigate to the TreeJuxtaposer downloads page http olduvai sourceforge net tj download shtml At the top of the page you should see a link to launch the WebStart Click this button to launch the WebStart 3 Load Context Tree and pre computed Phylogenetic Tree If you have not downloaded and extracted the contents of the zipped AlphaAndGammaProteobacteria package from the Facciotti lab website please do so In the extracted package you should discover a file titled AlphaAndGammaProteobacteria AlphaAndGammaProteobacteria nwk This is a whole genome phylogenetic tree In the TreeJuxta
39. specifying file paths of individual genome files please be sure to either specify 1 The absolute path or 2 The path relative to the directory from which JContextExplorer was launched JContextExplorer will be unable to import files if the file paths are not correctly specified Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 13 aoe GFF File Type import Settings Types to Include in Genomic Groupings Types to Include for Display only CDS mobile_element tRNA IS_element rRNA Add Remove Add Remove Instructions The third column of a GFF file describes each annotated feature s biological type For example coding regions E often have a type designation of CDS or gene and transfer RNA often have a type designation of tRNA This tool allows you to specify how to handle different types of annotated features In general among all possible feature types you may specify 1 The types that should be retained for both genomic grouping computation and display A 2 The types that should be excluded from genomic grouping computation but retained for display and Y Proceed to GFF import with these type processing settings GFF File Type Import Settings The third column of a GFF file describes each annotated feature s biological type For example coding regions often have a type designation of CDS or gene and transfer RNA often have a type designation
40. uster ID Show Coordinates Show Surrounding Before 1000 nt After 1000 nt Stop U Type M Annotation EA Strand Normalize Color Surrounding 4 Update Contexts This is an example of the Context Viewer Multi Genome browser frame This frame may be launched from the main frame see Launching Subordinate Windows and Selecting Nodes page 23 When launching this frame a set of leaves on a context tree must also be selected The purpose of this frame is to visualize the genomic groupings associated with the leaves on the active context tree Annotated features are rendered as colored rectangles colored according to common homology cluster ID number or common annotation depending on how the context tree was generated resting either above for plus stranded features or below for minus stranded features a single black line in the order they appear in the associated annotated genome Facciotti Lab UC Davis 451 Health Sciences Drive Davis CA 95616 37 The associated node name is printed above and to the left of each rendered genomic segment The ContextViewer is an active frame Left clicking right clicking and center clicking on individual genes and parts of the frame do different things Individual Option sub panes in the bottom left bottom center and bottom right also have interactive effects Gene Information Start M size M Cluster ID Stop Type M Annotation This is the Gene Infor
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