user manual
Contents
1. m 13 Ihe onthe seats cde enne p iud 13 Load map expression mto an empty Network senera a IRR SPEO Re OE e ES Eae anaE oera Ear aTa 15 ISepio ve ETO O ea E EE E A E E E ban E A 17 Load expression with an existing NetWork 17 Clans 19 Chanec de ex ptesstoOU 2 1018 BID eee eee E een eer ern rer ere 19 Export the network as SVG Scalable Vector Graph format 21 General SCTE MS OU NetWork 22 Doreenshotor the Same Network 18 the VG seseina in OEE Ea AEE AEEA EEO ETARE 23 Ffar e keda E e E E E E E A gn AEE E T E gem pete EN E 24 SVG file of the Same Network with Overlaid Expression 25 ID REUS RN ER mm 26 DI 26 Pie 26 DAU r 29 Loa DMa ms 29 ETFOP REDOTUNE ere er NE 29 Load KEGG Pathways Browse and Load KEGG Pathways From the VisANT s home page shown below select the species click the Browse KEGG Pathways button E VisANT An integr2. Quer Selected rear ornithine Quen intemal Connections Yiew Forced Nodes Query hormalizatian Filters Layout Available Links Label Protein Gene with Official Name H Label L Expression Plot Select Linked Modes Delete Selected Modes ka species Saccharomyces cere Save as the Image Grouping Duplication Postion Operation Ado Properties N 398 8N 1 E38 SE It takes 16 milliseconds by select the menu for pathway 00220 it will be loaded into VisANT Pal VisANT File apened http www genome jp kegg xml sce sce t zz xml File Edit View Filters Layout Modes MetaGraph Topology Options Expression Plugins Help vel imiz ati i Weight Cutoff to img Edge Optimization E mee ES Expression Plot C Labels 0 Quick Tip Help Zoom Pan Zoom Clear Zoom Back Rest Fit to Page 2 gt 030 species 000419 Saccharomyces cere w s con17 0 us COS59o36 i MOZ CO11865 i MAPODOBD Y L d N x KEGG Pathway MAF 00220 C040 Urea cycle and metabolism of amin 96 8 1 E111 SE Ittakes 31 millisecands Pathway Expansion If the loaded pathway has links to other pathways these pathways can be expanded by double clicking corresponding pa
3. Note Manual arrangement of the layout may be required For easy management pathway nodes can be contracted by double clicking over them Pathway Navigation and Enrichment Compare Pathway Visualized in VisANT with the Pathway Image in KEGG VisANT provides convenient functions for this purpose For each node shown in the pathway node there is a menu directly link it back to the colored KEGG pathway image as shown in the following figure SKIF pTX2 CREBBP RSTS 51 HBPSUHL diee Query Selected l AIRLESS B Query Intemal Connections CIR HDA M iew Forced Nodes Query Filters Name Normalization Layout Expand Pathway Save as the Image GO Annotation Pa oawmmE EEEENFEEGEGNN FI i z E gt E Note Sd AP y Recre tase complex Enrich Pathway Using Expression Data GeneRecommender Plugin GeneRecommender discovers new genes with similar function to a given list of genes the query already known to have closely related function It ranks genes according to how strongly they correlate with a set of query genes in those experiments for which the query genes are most strongly coregulated Invoke GeneRecommender To searching for coexpressed genes using GeneRecommender select the nodes in the network and invoke GeneRecommdender as following figures Modes MetaGraph Topol
4. File Format As usual VisANT recognize the format of the file by its internal context There are two section of the file File Header All lines starts with the are named as file header as shown in the following example The header must have the first line and last lines shown below all others are optional ID Mapping AddNewNode false following URL is for swiss prot database linkout swiss prot UniProtKB Swiss Prot entry http ca expasy org uniprot 26 ViSANT_ID swiss prot YILO47C P40528 YCLO32W P25344 YLR286C P29028 YDR264C P39010 YLR362W P23561 The file must start with the 110 Mapping line so that VisANT can load correct parser There is one parameter AddNewNode for this line If this parameter is true then those nodes that do not match any nodes in the network using the the first column of the data section will be added to the network otherwise they will be ignored This parameter is optional the default value is false The 2nd line in the above example is comment line you can have as many comment lines as you want The 3rd line tells VisANT to have an link out menu for those nodes that has the swiss prot IDs It must follow the format ID Name Menu Name web URL Where ID Name is the database id listed in the D List line once matched a menu will be created under Nodes Available Links using the name specified by Menu Name as shown in the following figure 27 Mode s H Query Selected Qu
5. p 65 M 2 25 a 77 Ey Re y NV AR WC p f o 1 5 um F n oes qi f ai A ds Screenshot of the Same Network the SVG format 23 shown using Adobe SVG viewer St p nina 2 E t LAT doe RN unu FFF Lm m a b i ARS be EE A 200 Wn NS ex Zoomed SVG file SVG allows graph to be freely zoomed with same quality 24 N T M f SN m B 4 4 N Wie SVG file of the Same Network with Overlaid Expression Data 25 new feature in this release allows expression profile to be shown as a node ES i IU _ DIS L o We k S NN 771 ID Mapping File This file format is designed to allow user to add various database IDs as well as alias and functional descriptions to the corresponding proteins genes of a network in a batch mode Aliases and functional descriptions will be shown in the tooltip when mouse over the node aliases and IDs are searchable in VisANT In addition it also allows each database Ds to be mapped to an URL so that corresponding web links can be directly loaded into browser from VisANT under Available Links menu of the Nodes menu
6. names of the node used in VisANT can be be exported 28 Data Section The data section is relatively simple Each line must be Tab delimited The first column is the ID Name of the node Use space as the value of the column if the certain IDs are not available for some nodes alias If multiple alias exist use as the delimiter description No Tab allowed in the description A more detailed example of ID Mapping file is shown below and can be downloaded here Note Copy amp Paste following text may not work please download file directly from above link ID Mapping AddNewNode true PDB id Protein Data Bank http www rcsb org pdb explore do structureld Gene3D Gene3D http cathwww biochem ucl ac uk cgi bin cath GotoCath pl cath swiss prot UniProtK B S wiss Prot entry http ca expasy org uniprot VisANT_ID swiss prot description id alias Gene3D YILO47C P40528 Membrane multi pass membrane protein SYGI YCLO32W P25344 Involved in growth arrest during conjugation May interact with the G protein alpha subunit 1Z1 V STES0 G3DSA 1 10 150 50 YLR286C P29028 Soluble cell wall protein 2 CTS1 YDR264C P39010 Ankyrin repeat containing protein AKR1 AKRR G3DSA 1 25 40 20 YLR362W 23561 Serine threonine protein kinase 1X9X STEI1 G3DSA 1 10 150 50 Load ID Mapping file The file can be directly loaded loaded into VisANT using File menu As usually the context of the file can also directly copy paste to Add textbox and load it
7. shown below which will load the latest KGML of corresponding from KEGG and all user customization will be retained m m pul 10 Mode s k Update from Available Links Overlay Expression Data over the Network Note this feature is only available for VisANT2 5 and above The format of expression data The full format of the expression is shown as following 13 Expression log2RAT mmm 19751 0 36 1 992 0 51995 19055 URN 190959 1 493592 1 595552 11651 0 05 705 11652 0 634509 0 624509 12914 517516 Bad SL 19055 1495926097 1 996697 19059 1 060696 1 661656 19393 LOG Ue 15 HOS fcomments can be anyhere 12914 0 00423 0 00423 12914 e 8062 1 000021 11652 0 639012 0 039012 11651 392924 Q 5929 Note In the case that VisANT is run as an online applet Add box shown below 12914 11652 11651 Expression This line must kb fany line starts with will bi vou may have a line to list t loge 138751 O 6799 2 19055 O 17261 19055 1 493562 11651 0 05703 11652 0 634509 12914 0 17516 19055 1 596697 19055 1 661656 12353 0 015109 comments can he 12914 0 00323 12914 O c06621 11652 0 638012 11651 0 392922 0 87992 0 17281 1 493562 0 05703 0 634509 17518 596697 651656 0 013109 anyhere 0 00423 0 86621 0 635012 0 392922 Pe Oo the above data 1s stored in the file named as mmu txt For user s conv
8. the input box as shown below Va isANT File opened http visant bu ed File Edit View Filters Layout Please enter the URL address of the network ltp ilwww genome jp keggixmlihsalhsaD43 E Note for VisANT 3 0 or below URL must be typed in when VisANT is run as an online Applet Open Ctrl O pen URL Etrl R esr mal 1 am Load Pathway by Searching It s ID If the KEGG ID is known then it can be loaded by type in the MAP ID in the searching box For example for the pathway shown above its ID is 04330 and can be searched using name MAP04330 Note multiple pathway IDs can be typed in the search box Load Pathway when A Node Is Involved in A Pathway When a protein gene is searched in VisANT or its IDs is resolved through Name Normalization service VisANT will tell whether this protein gene is involved in one or more KEGG pathways In such case VisANT can loaded pathway directly as shown below ARGS is searched for interaction in this example opened start_up xml File Edit View Filters Layout Nodes MetaGraph Topology Options Expression Plugins Help m T it imiz ati i Weight Cutoff to Cm Edge Optimization E iE anit Expression Plot Labels Auto Fit j Quick Tip Help Zoom Zoom Out E dit zoom Back Search Compound Pathway and ProteinGere Search arg gt
9. Link Using Same Browser Fine Arts Transparent Quick Tip Edge Weight Visualization Je S055 16 Then select all nodes and do name normalization here is the resulted network VisANT File opened start E File Edit View Filters Layoul Modes Edges MetaNetwou Topolog Option PIENE Plugins Help ight i imiz ati 1 Weight Cutoff OS to Edge Optimization 55521 1655 T E vj Labels Auto Fit e Quick Tip Help we Select oom Pan Zoom Out wet Clear E Eac S U Magne elated Botulinum substrate 1 Alias AL023028 DSERTDSSGE NGISTS45 Expression 0 013109 Total links and 0 visible It takes 16 milliseconds 5 8 5 E 0 SED Remove expression data Expression data can be easily be removed from the network through corresponding menu i iu ession Plugins Help Load Expression Matrix File Remove expression data fram Load expression with an existing network Let s first load a network named exp xml then remove the expression data then load expression file named expression_simplest txt the resulted network is shown as following 17 pu YALO25C a Expression 1 89 4 Total links and D visible The new or matched nodes are selected and colored corresponding to their expression value The new added nodes are laid out using a circle Note I
10. Note This is just partial of VisANT manual related with the NAR 2007 submission Please visit http visant bu edu for the full user manual Load ITE Gap 45 cans gnc cee 1 browse and Load KEGU Pati w METTEC 1 Load Netw Oph Pathway Cle in Web BU Pc ener 3 Load Pathway when A Node Is Involved in A Pathway 4 Pathway EDAD ION eae ERI IO P DNUI 6 Pata ay Navies ation E 7 Compare Pathway Visualized in VisANT with the Pathway Image in KEGG ccccccccsssseseeeceeeeeeaeeeseeeeceeeeeaaeeseeeeeeeeeas 7 Ponch Pathway Usine Expression Ala 8 Se ee mn DOE TIU GEL ese ee 8 RU A FO T E 11 Ponch Pathway Usine Miter acim 12 Add Nodes to the Existine Metanode xoccsssocsnssevsacerssueseuaaddvacennodvsvnnsennnsanesdudeinesenensnnesaudacencauesnunedussioese E aa 12 ty 13 Overlay Expression oyver diem C
11. The expression plot will only be shown if the metanode is contracted If more than one child nodes have the expression profile the average expression profile will be shown using the black thick line Following figure shows the expression plot of the above mentioned pathway in the zoom in state 4010 For the metanode the cursor and value points to the average expression value Note Similar to node label the expression plot can also be turned on off using individual control in the nodes menu 20 gc P CRZ c FALDA 12716 Edges k uc e eee ae i Node s M Query Selected Edit Query Internal Connections View Forced Nodes Query Filters Normalization 2 Layout Expand Pathway p Save the image GO Annotation j Help Available Links Label Protein Gene with Official Name IM Label H Expression Plot _ Select Linked Nodes Delete Selected Nodes The individual control of the expression plot is saved in the visML file Export the network as SVG Scalable Vector Graph format Note this feature is only available for VisANT 2 51 or above Note this feature requires internet connection To activate this function select the corresponding menu under File menu as shown in the following figure 2 isANT Open Filerexpression s g xml Edit View Filters Layout Export as Tab Delimited File Export As SVG File VISANT network as a high qua
12. ative platform for network pathway analysis Microsoft Internet Explorer File Edit View Favorites Tools Help x B _ Search des e 0 TM j ome ews Search Run visan a Gene Protein name ID in species Saccharomyces cerevisiae gil Search for Interactions KEGG Pathways Help Tutorials Samples Statistics Run as Local Application Download Documents m 4 k See internet 7 and corresponding KEGG pathways will be listed as following click the Graphics link of interested pathway as shown below E VisANT An integrative platform for network pathway analysis Microsoft Internet Explorer File Edit View Favorites Tools Help eL d x B 2 Search Vp Favorites ec a rative Visual fool Ter Biological Networks ar Search Fun visan Documents Community SC UUSOU EMU graphics metTaponsm sceQ0360 xml html graphics Phenylalanine metabolism sceD0380 xml html graphics Tryptophan metabolism 0400 xmi html graphics Phenylalanmne tyrosine and tryptophan biosynthesis xml html graphics Urea cycle and metabolism of amino groups E javascript parent 00220 xml Internet Corresponding pathway will be loaded into VisANT VI TisANT Open File http vi
13. by clicking Add button as shown below SPDB Protein Data Bank h sisene3ll Gene3D http cat Szwisz prot liniProtEB Swi vVizAHT III Sw k Parsing Error Reporting System To improve the reliability of the integrated distributed system such as GeneCommender plugin and ClueGene plugin VisANT allows user to report the critical errors to the authors of the plugins as well as VisANT development team so that the error can be fixed as soon as possible Following figure shows an example 29 VisANT Error xj ViIsANT has account following errors Can not open the specified URL http iisy sbio soe educgi binClue Genefcluegene va pl java io FilellotF oundEx ception http Ns shio sn0e ucsc ecducgi bin Clue Genefcluegene va plxxx Quer sting 95841 51107 5664 5663 23385 Do you want to report this error to VISAMT group Your report can speed up the process to fm the errors aw se If Yes is selected an email will be generated and sent out Following is an example of such email VisANT Error Report Component of the error PluginGeneRecommender VisANT versionz2 7 Java version 1 4 2 05 Operation system Windows XP Can not open the specified URL http disco cse ucsc edu 8001 qrforvisant search species hsa amp key T yoe loc amp showScore Y amp nTopGene 10 amp nTopExp 50 java lang NumberFormatException For input string Error encoutered while creating
14. case for all expression files we can simply drag the slider shown in above figure to change the experiments The name or the sequential number of the experiment will be shown at status bar Click on the empty place of slider will change experiments one by one The change of expression experiments can also be animated by click on the Play button as shown above e Expression Plot So what we can do if we want to view all expression experiments of a given set of nodes The answer is simply turn on the Expression Plot checkbox as shown in above figure Here is the pathway with this option is on 19 Fiep path arami File Ect View Fitters Layout Nodes Edges MelaNetwork Topology Options Expression Plugins Help e Expression Plot Weight Cutof gto 1H gt timization j E _ Imm ES Labels Quick Tip Select t Auto Y 1 014 Saccharomyces em d pa AS Diele i Total 77 links and 1 visible Lal N 89 8N 0 E75 Expression experiment 107 The cursor and the value in the node represent the expression value of the current experiment 107 experiment The size of the expression node can be changed either by define the node size or zoom in out For the metanode the expression plot is a recursive sum of its child nodes
15. enience it 1s also listed here This line must be presented tany line starts with will be treated as comments fyou may have a line to list the name of experiment separated by TAB delimit Your data 0 0 636012 0 392922 N B SN B SE U missing value of expression can be represented as NA above data can be directly copy paste to Click Add button to add the data 14 Note In general any VisANT supported data can be pasted to Add box and VisANT will lod it correctly But there are exceptions For example the simplified format shown below will not work correctly this is because the default format for Add box is edge list if VisANT can not find any hints about the format of the data The format can be simplified following shows a simplified format XYALXIUTiITI1 53 OS OS Nm d d Oe XALIUZW LH nli U 3 OOD USS 0 45 0 n i FELOOSW De 1 de De LH 34 YRLOOSW Oe OT ODE OO XALIUSC z2 805 4 44 LLL OO Oe H 55 LH L3 FALOU M a YALUUSW 0 19 0 45 O lt 69 0 354 O 65 U 48 YALOOSW 0 05 U 18 U 15 O 06 0 19 O e ALOJO OOS o LHEESONIJGG Oa oe Oe YR LOT OO H lza 0 H 45 SE AW Ded SOO ORGS 4 above data is part of the data stored in expression_simplest
16. ery Intemal Connections M pen Forced Nodes Query Filters Name Normalization Layout Expand Pathway Save as the Image GO Annotation Hep Available Links hs ony 2 Label Protein Gene with Official Name Proteini Mapped IDs d UniProtkE Swiss Prot entry 40528 STG1 YEAST Protein 5751 Microsoft Internet j Fie Edt Hel htesllca expasy oralun http ica expasy orgluniprofe 85 Prot entr Ty P40528 Swiss rot BlastP search m URL Entry history Tools Entry info Name and origin References Comments Cross references Keywords Features Sequence Tools Note most headings are clickable even if they dont appear as inks They link to the user manual or other documents Entry information X See LI GV As shown in the above figure the actual URL will be the web URL ID Name For an example the corresponding URL for node YILO47C 15 http ca expasy org uniprot P40528 The last line of the file header in the above example list the total columns of the IDs The first column must be VisANT_ID which represents the name or ids that can be uniquely identified by VisANT in the current network This line must be Tab delimited Although the name of the IDs can be determined by the user there are two key names that are reserved by VisANT alias and description See example below for more detail Note The default
17. f the expression data contains nodes that are not in the network these nodes will be arranged into a circle and put in the cent of the network To remove these new added nodes you can either move whole network into a corner or group them We can also easily mapping expression to the KEGG pathway To illustrate clear the network and search for keg pathway map04010 and then load expression data expression_data TXT this data file is 8M and will take about 3 minutes to load After removing the nodes do not belong to the pathway the network will look like following the resulted network has been saved as exp_pathway xml 18 drow YBR200WW y NL ee cMyeicooze duse S gt LM Kyoroszw Sree ON yenusc w _ 2 5 __ noose Mei j qu ge dir Change the color mapping By default the maximum of the expression value is mapped with green color and and minimum value is mapped with red color The mapping can be changed by clicking on the color button shown below left for minimum and right for maximum Dod 79 a Expression Plot Play Change the expression experiment If the expression has multiple experiments which is the
18. li gt Rank ClueGene Plugin ClueGene uses the pattern of how genes cluster together in different experiments to recommend new genes in a pathway ClueGene bases its recommendations on the query set and on a cluster compendium Each experiment series is clustered independently The collection of clusters from all the experiment series constitutes the cluster compendium Each gene g in the genome is given a co clustering score C g A cluster c in the cluster compendium contributes to the score of g if g is a member of c The contribution of c to the score of g is proportional to the number of query genes found in the cluster c and inversely proportional to the size of the union of the cluster c and the query set to down weight co occurrence of g and the query in the same cluster by chance A gene with a higher co clustering score is more likely to participate in the pathway of the query genes than a lower scoring gene Note that scores can only be compared for the same species cluster compendium and query set In other words a gene has a higher score and thus is more highly recommended if it is found in small clusters along with query genes 11 The interface as well as the operation of the ClueGene plugin is similar to the GeneRecommender plugin please reference corresponding sections for detail Enrich Pathway Using Interaction Data Interaction data either computational or experimental can be easily queried against Predictome Followi
19. lity Sv file VisANT will then send the current network to VisANT server which will translate the network in the SVG format The SVG data xml file will then be shown in browser as shown in the following 21 http visant bu edu applet tmp visant visml9 svg Microsoft Internet E File Edit View Favorites Tools Help gt E x B A Search x p Favorites Address http visant bu edu applek EmpJsisank wisma svg Geoge C v _ ot v lt xml versionz 1 0 encadingz UTF 8 2 lt IDOCTYPE swg view Source for ful doctype d svyg xmlns xlink http www mw 3 org 198990 xlink style rendering auto stroke black stroke linecap square st strake dasharray none font weight normal stroke wi font size 12 stroke dashoffset 0 image rendering aul preserveAspectRatio xMid YMid meet zoomAndPan mag contentStyleType text css gt lt l Generated by VisAMT http visant bhu edu gt lt defs id 2 genericDefs gt g defs id defs 1 gt image width 80 height z 8D id imagel Please save the returned SVG file in local disk and then loaded it into corresponding SVG viewer such as Adobe SVG Viewer free Or you can try open source SVG edit Inkscape Like postscript SVG enables you to have high quality pictures of the network Here are some examples you can compare General Screenshot of A Network Tr spe MMC
20. ng figure shows an example to query the intra connectivity between top 10 coexpressed genes returned by GeneCommender NUMB SM SKIP E QU CRE BBP RS RS 5 7 54 JAG1 AGS 7 um m Eg G64 a at af AIRLESS P pnm ge 3 SAD ANIA s GROUCHEDSCIR c BU a a9 pe mE rzecretase sori plas M 1 HDAC RPDLT MAPD330 uL m Mode s E dit Query Intemal Connections thraw Quer Selected V ieu Forced Nodes Query boss SKIIF CRE BBP R5 RS Hide Selected Delete Selected Edges rzecrpetaze r MAPOAS SO View Literature Evidences Filters Publi ed M0010 1 Literature evidences of the detected interactions can be easily launched into browser as shown above Add Nodes to the Existing Metanode Pathway To add nodes to an existing metanode simply select the nodes and drag then over the metanode as shown in the following figure 12 A confirmation window will be popped out select Y will add selected nodes to the metanode as shown above Note if one of the selected nodes belongs to a metanode which is not selected VisANT will ignore this functionality Note to add a node already belongs to a metanode to another metanode duplicate the node first and then drag the duplicated instance to the target metanode Update KEGG Pathway KEGG pathways saved before in VisANT can be updated as
21. ogy Options Expression Plugins Edge Optimization d x Load Expression Matrix File o Exp Gene Herr mmen der 3 e ClueGene E e n E JAG1 AGS i ENT f senz a 2 Ls gero T 4 YisANT Plugin Gene Recommender JC REA Gene Recommender Number of Top Genes 10 Number of Top Expenments u ww Species Homo sapiens Key Type Entrez Gene ID Quen Gene lais coexpressed genes k Mo data to draw Group the coexpressed genes Get Selected Nodes Search Select Input Nodes Reset Close Input Parameters of GeneRecommender Query genes This field list the IDs of genes used for GeneRecommender It can be directly typed in or copied pasted from other place if the genes to be queried are not in the current network Otherwise click Get Selected Nodes to get the selected nodes in the current network as the query genes After this button is clicked VisANT will resolve the name of the selected node first and then put them in the field as shown below Top number of genes This is the number of best coexpressed genes that will be returned by GeneRecommender Top number of experiment GeneRecommender will return the expression values of the number of experiments specified by this parameter In addition the coexpression scores are also calculated based the e
22. sant bu edu 1 sample kegg sce sce uuzzu ml File Edit View Filters Layout Hodes Edges MetaGraph Topology Options Expression Plugins Help _ Weight Cutoff to H Edge Optimization E i m Expression Plot _ Labels Auto Fit Quick Tip oom In coom Out foom Back Fit to Page Search Compound Pathway and Proteinisene Search MAPOOSSO MAPOOOSO MAPOD252 4 yesa M AFPOD230 099169 1 n species Saccharomyces Cerevi am Please Register ju dont account 472 Pi Logi n ogin n n Delete Open E d Share a yeo0134 n SPE3 m Pathway MAPOO220 Urea cycle and metabolism of ami contains 40 nodes with total 0 eda 0251 COU 15 Collapsing KEGG groups Java Applet Window Note Multiple pathways can be loaded Note It is possible that some pathway s default location is out of the visible draw region in VisANT In such case clicking on the FitToPage button at left control panel will easily make it visible Load Network Pathway through Web URL VisANT can load any supported data such as VisML KGML Edge List etc from a Web resource To load KEGG pathway from the Web resource simply select the menu Open URL menu and copy paste the URL into
23. the request directory Please report the problem to cchen cse ucsc edu Query string 23385 5664 5663 55851 51107 java lang NumberFormatException forlnputString NumberFormatException java 48 java lang Integer parselnt Integer java 468 java lang Integer parselnt Integer java 518 cagt bu visant plugin PluginGeneRecommender searchCoExpression PluginGeneRecommender java 278 cagt bu visant plugin PluginGeneRecommender run PluginGeneRecommender java 161 java lang Thread run Thread java 534 Please email VisANT zlab bu edu if you have any questions about this email 30
24. thway node Following figure shows the result when the pathway node MAP00910 is double clicked after 220 is loaded VI VisANT File opened http www genome jp kegg xml sce sce us10 xml File Ean View Filters Layout Modes MetaGraph Topology Options Expression Plugins Help Wei ht Cutoff pid Sto 4 15 Edge Optimization Expression Plot i H pi x Exp 10 Ci Label vi Auto Fit CARI LPH15 els Fi Ds oe 00011 Quick Tip p Heb Help ARd2 5 HRB5T4 oom Zoom Out Zoom Out Es napooza ES Clear o Fit to Page o UT e 8 we a c et Search pc uL 01137 00019 XU Le E TUERI 4 oto a 0960 E ON MAPOOAT n n 00170 DOE APDOZS1 c p T Dm eor S Saccharomyces cere ww B w ALD5 inm m Please Register A CMM 00324 m If you dont have an account M Bue Available Files Pul T mo Ee p __ ET m ee b Login FE E Ie E hd ET 0 0 nn 9 RT EN cs n ae 1 nc E t shared Files Your data Add Pu KEGG PathwayMAPO0910 um 9 Nitrogen metabolism contains is nodes with total edges N 80 8N 1 E 115 Collapsing KEGG groups
25. txt Note any type of data can be imposed over the network as long as the format is correct Load map expression into an empty network Expression data can be loaded into VisANT through following menu Load Expression Matrix File Remove Expression Select Nodes Based on Expression Range following figure shows the network when mmu txt 15 loaded 15 E VisANT File opened start_up ml E _ Dj x i File Edit View Filters Layoul Kodes oye MetaNetwoi Topolog Option Expressio Plugins Help wastcuer oE to 15 Labels Auto Fit de 1641 er 11652 Expression 0 538012 19055 Total 777 links and 0 visible ao lm mt x Bees I RE N 5 8N 0 E 0 SE 0 Expression experimentlog2RAT Note Please select correct species Mus Musculus before loading the expression data because the expression data itself have no information of the species The nodes are identified as Entrez Gene ID in above example and the node color represents the expression value The actually expression value of the current experiment can be known by moving mouse over the node The current experiment name is shown in the status bar We can pull the detailed information of the nodes using Name Normalization Make sure that you select case insensitive for mmu ior Expressio Plugins Help Allow Popup Dialog Open
26. xpression values of these experiments Group the coexpressed genes This option is useful when selected genes are in a large interaction network as it will group the returned top number of coexpressed genes It is not useful in the case of pathway enrichment because these nodes are already grouped in the pathway Searching and resultsnavigation Click the Search button will start the searching process in the background and all buttons will be disabled until the searching is finished Once finished the score plot of top number of coexpressed genes will be plotted and new genes in the returned top coexpressed genes will be arranged into a circle as shown below Nodes of these returned genes will be colored according to the expression value of the first experiment To link the score in the plotter to the corresponding genes select the spots in the plotter and the corresponding nodes will be selected as shown below 10 a i Sa i VM Mo C PSENT p oe 1 E S i N 585 j ETBE m E 1 4 MisANT Plugin Gene Recommender isl Gene Recommender Number of Top Genes 10 Number of Top Experiments 40 T Species Homo sapiens Key Type Entrez Gene ID Quer Gene ld sy z3385 HCSTH Top coexpressed genes 55851 PSEHEN 5664 877 83 S663 PSEW1 51107 APH1A D 616 55 555 26 493 98 432 70 37141 310 13 248 84 187 56 126 27 64 00 0 1 2 3 4 5 7 8 9
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