Cytoscape test3: Difference between revisions
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request.send(null); | request.send(null); | ||
var xml = request.responseText; | var xml = request.responseText; | ||
$(function(){ | $(function(){ | ||
//var xml = '<?xml version="1.0" encoding="UTF-8"?><graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"> <key id="zscore" for="edge" attr.name="zscore" attr.type="double"/> <key id="promoter" for="edge" attr.name="promoter" attr.type="string"/> <key id="motif" for="node" attr.name="motif" attr.type="string"/> <graph id="G" edgedefault="directed"> <edge id="e1" source="ADNP" target="EHF"> <data key="zscore">1.855803</data> <data key="promoter">chr11:34642612..34642646,+</data> </edge> <edge id="e2" source="ADNP" target="EHF"> <data key="zscore">2.728882</data> <data key="promoter">chr11:34642656..34642667,+</data> </edge> <edge id="e3" source="ADNP" target="SIX2"> <data key="zscore">1.689851</data> <data key="promoter">chr2:45236540..45236577,-</data> </edge> <edge id="e4" source="ADNP" target="ZFHX4"> <data key="zscore">2.786958</data> <data key="promoter">chr8:77593474..77593612,+</data> </edge> <edge id="e5" source="ARNTL2" target="NFIX"> <data key="zscore">2.512098</data> <data key="promoter">chr19:13106214..13106382,+</data> </edge> <edge id="e6" source="ARNTL2" target="ZNF507"> <data key="zscore">4.290077</data> <data key="promoter">chr19:32836499..32836551,+</data> </edge> <edge id="e7" source="ARNTL2" target="ZNF593"> <data key="zscore">6.795832</data> <data key="promoter">chr1:26496382..26496457,+</data> </edge> <edge id="e8" source="ARNTL2" target="LYAR"> <data key="zscore">3.218736</data> <data key="promoter">chr4:4291861..4291913,-</data> </edge> <edge id="e9" source="ARNTL2" target="MATR3"> <data key="zscore">5.344587</data> <data key="promoter">chr5:138609782..138609826,+</data> </edge> <edge id="e10" source="ARNTL2" target="PLAGL1"> <data key="zscore">1.795280</data> <data key="promoter">chr6:144329384..144329405,-</data> </edge> <edge id="e11" source="ARNTL2" target="FOXP4"> <data key="zscore">4.201205</data> <data key="promoter">chr6:41514078..41514158,+</data> </edge> <edge id="e12" source="CDC5L" target="SOX15"> <data key="zscore">2.026144</data> <data key="promoter">chr17:7493405..7493419,-</data> </edge> <edge id="e13" source="CDC5L" target="TFAP2C"> <data key="zscore">2.842422</data> <data key="promoter">chr20:55204351..55204377,+</data> </edge> <edge id="e14" source="CDC5L" target="PCBP1"> <data key="zscore">3.387780</data> <data key="promoter">chr2:70314579..70314590,+</data> </edge> <edge id="e15" source="E2F1" target="E2F8"> <data key="zscore">13.881050</data> <data key="promoter">chr11:19262421..19262455,-</data> </edge> <edge id="e16" source="E2F1" target="PAX6"> <data key="zscore">7.520784</data> <data key="promoter">chr11:31832610..31832639,-</data> </edge> <edge id="e17" source="E2F1" target="PAX6"> <data key="zscore">4.551613</data> <data key="promoter">chr11:31832658..31832681,-</data> </edge> <edge id="e18" source="E2F1" target="DDB2"> <data key="zscore">8.634349</data> <data key="promoter">chr11:47236584..47236679,+</data> </edge> <edge id="e19" source="E2F1" target="CREBZF"> <data key="zscore">7.967076</data> <data key="promoter">chr11:85376121..85376181,-</data> </edge> <edge id="e20" source="E2F1" target="E2F7"> <data key="zscore">8.834300</data> <data key="promoter">chr12:77459306..77459365,-</data> </edge> <edge id="e21" source="E2F1" target="TFDP1"> <data key="zscore">12.764142</data> <data key="promoter">chr13:114238997..114239077,+</data> </edge> <edge id="e22" source="E2F1" target="ZNF828"> <data key="zscore">13.732920</data> <data key="promoter">chr13:115079949..115080022,+</data> </edge> <edge id="e23" source="E2F1" target="CTCF"> <data key="zscore">10.989668</data> <data key="promoter">chr16:67596417..67596497,+</data> </edge> <edge id="e24" source="E2F1" target="HOXB7"> <data key="zscore">5.976186</data> <data key="promoter">chr17:46687959..46688007,-</data> </edge> <edge id="e25" source="E2F1" target="DNMT1"> <data key="zscore">14.442942</data> <data key="promoter">chr19:10305581..10305646,-</data> </edge> <edge id="e26" source="E2F1" target="ZNF473"> <data key="zscore">12.242552</data> <data key="promoter">chr19:50529247..50529296,+</data> </edge> <edge id="e27" source="E2F1" target="ZSCAN22"> <data key="zscore">9.279835</data> <data key="promoter">chr19:58838369..58838439,+</data> </edge> <edge id="e28" source="E2F1" target="STIL"> <data key="zscore">11.896066</data> <data key="promoter">chr1:47779762..47779827,-</data> </edge> <edge id="e29" source="E2F1" target="ZNF644"> <data key="zscore">3.675427</data> <data key="promoter">chr1:91487553..91487612,-</data> </edge> <edge id="e30" source="E2F1" target="E2F1"> <data key="zscore">11.184354</data> <data key="promoter">chr20:32274179..32274213,-</data> </edge> <edge id="e31" source="E2F1" target="GMEB2"> <data key="zscore">3.649241</data> <data key="promoter">chr20:62258402..62258464,-</data> </edge> <edge id="e32" source="E2F1" target="TFDP2"> <data key="zscore">6.243192</data> <data key="promoter">chr3:141868293..141868355,-</data> </edge> <edge id="e33" source="E2F1" target="TFDP2"> <data key="zscore">6.980334</data> <data key="promoter">chr3:141868357..141868393,-</data> </edge> <edge id="e34" source="E2F1" target="MATR3"> <data key="zscore">5.335442</data> <data key="promoter">chr5:138629349..138629386,+</data> </edge> <edge id="e35" source="E2F1" target="MATR3"> <data key="zscore">9.145348</data> <data key="promoter">chr5:138629417..138629446,+</data> </edge> <edge id="e36" source="E2F1" target="E2F3"> <data key="zscore">11.747304</data> <data key="promoter">chr6:20402102..20402152,+</data> </edge> <edge id="e37" source="E2F1" target="SOX4"> <data key="zscore">5.461751</data> <data key="promoter">chr6:21593973..21593988,+</data> </edge> <edge id="e38" source="E2F1" target="TCF19"> <data key="zscore">11.251513</data> <data key="promoter">chr6:31126291..31126399,+</data> </edge> <edge id="e39" source="E2F1" target="GRHL2"> <data key="zscore">3.270715</data> <data key="promoter">chr8:102504651..102504683,+</data> </edge> <edge id="e40" source="E2F1" target="GRHL2"> <data key="zscore">4.898434</data> <data key="promoter">chr8:102504690..102504704,+</data> </edge> <edge id="e41" source="E2F1" target="MYC"> <data key="zscore">7.263588</data> <data key="promoter">chr8:128748470..128748487,+</data> </edge> <edge id="e42" source="E2F3" target="E2F8"> <data key="zscore">13.881050</data> <data key="promoter">chr11:19262421..19262455,-</data> </edge> <edge id="e43" source="E2F3" target="PAX6"> <data key="zscore">7.520784</data> <data key="promoter">chr11:31832610..31832639,-</data> </edge> <edge id="e44" source="E2F3" target="PAX6"> <data key="zscore">4.551613</data> <data key="promoter">chr11:31832658..31832681,-</data> </edge> <edge id="e45" source="E2F3" target="DDB2"> <data key="zscore">8.634349</data> <data key="promoter">chr11:47236584..47236679,+</data> </edge> <edge id="e46" source="E2F3" target="CREBZF"> <data key="zscore">7.967076</data> <data key="promoter">chr11:85376121..85376181,-</data> </edge> <edge id="e47" source="E2F3" target="E2F7"> <data key="zscore">8.834300</data> <data key="promoter">chr12:77459306..77459365,-</data> </edge> <edge id="e48" source="E2F3" target="TFDP1"> <data key="zscore">12.764142</data> <data key="promoter">chr13:114238997..114239077,+</data> </edge> <edge id="e49" source="E2F3" target="ZNF828"> <data key="zscore">13.732920</data> <data key="promoter">chr13:115079949..115080022,+</data> </edge> <edge id="e50" source="E2F3" target="CTCF"> <data key="zscore">10.989668</data> <data key="promoter">chr16:67596417..67596497,+</data> </edge> <edge id="e51" source="E2F3" target="HOXB7"> <data key="zscore">5.976186</data> <data key="promoter">chr17:46687959..46688007,-</data> </edge> <edge id="e52" source="E2F3" target="DNMT1"> <data key="zscore">14.442942</data> <data key="promoter">chr19:10305581..10305646,-</data> </edge> <edge id="e53" source="E2F3" target="ZNF473"> <data key="zscore">12.242552</data> <data key="promoter">chr19:50529247..50529296,+</data> </edge> <edge id="e54" source="E2F3" target="ZSCAN22"> <data key="zscore">9.279835</data> <data key="promoter">chr19:58838369..58838439,+</data> </edge> <edge id="e55" source="E2F3" target="STIL"> <data key="zscore">11.896066</data> <data key="promoter">chr1:47779762..47779827,-</data> </edge> <edge id="e56" source="E2F3" target="ZNF644"> <data key="zscore">3.675427</data> <data key="promoter">chr1:91487553..91487612,-</data> </edge> <edge id="e57" source="E2F3" target="E2F1"> <data key="zscore">11.184354</data> <data key="promoter">chr20:32274179..32274213,-</data> </edge> <edge id="e58" source="E2F3" target="GMEB2"> <data key="zscore">3.649241</data> <data key="promoter">chr20:62258402..62258464,-</data> </edge> <edge id="e59" source="E2F3" target="TFDP2"> <data key="zscore">6.243192</data> <data key="promoter">chr3:141868293..141868355,-</data> </edge> <edge id="e60" source="E2F3" target="TFDP2"> <data key="zscore">6.980334</data> <data key="promoter">chr3:141868357..141868393,-</data> </edge> <edge id="e61" source="E2F3" target="MATR3"> <data key="zscore">5.335442</data> <data key="promoter">chr5:138629349..138629386,+</data> </edge> <edge id="e62" source="E2F3" target="MATR3"> <data key="zscore">9.145348</data> <data key="promoter">chr5:138629417..138629446,+</data> </edge> <edge id="e63" source="E2F3" target="E2F3"> <data key="zscore">11.747304</data> <data key="promoter">chr6:20402102..20402152,+</data> </edge> <edge id="e64" source="E2F3" target="SOX4"> <data key="zscore">5.461751</data> <data key="promoter">chr6:21593973..21593988,+</data> </edge> <edge id="e65" source="E2F3" target="TCF19"> <data key="zscore">11.251513</data> <data key="promoter">chr6:31126291..31126399,+</data> </edge> <edge id="e66" source="E2F3" target="GRHL2"> <data key="zscore">3.270715</data> <data key="promoter">chr8:102504651..102504683,+</data> </edge> <edge id="e67" source="E2F3" target="GRHL2"> <data key="zscore">4.898434</data> <data key="promoter">chr8:102504690..102504704,+</data> </edge> <edge id="e68" source="E2F3" target="MYC"> <data key="zscore">7.263588</data> <data key="promoter">chr8:128748470..128748487,+</data> </edge> <edge id="e69" source="E2F4" target="E2F8"> <data key="zscore">13.881050</data> <data key="promoter">chr11:19262421..19262455,-</data> </edge> <edge id="e70" source="E2F4" target="PAX6"> <data key="zscore">7.520784</data> <data key="promoter">chr11:31832610..31832639,-</data> </edge> <edge id="e71" source="E2F4" target="PAX6"> <data key="zscore">4.551613</data> <data key="promoter">chr11:31832658..31832681,-</data> </edge> <edge id="e72" source="E2F4" target="DDB2"> <data key="zscore">8.634349</data> <data key="promoter">chr11:47236584..47236679,+</data> </edge> <edge id="e73" source="E2F4" target="CREBZF"> <data key="zscore">7.967076</data> <data key="promoter">chr11:85376121..85376181,-</data> </edge> <edge id="e74" source="E2F4" target="E2F7"> <data key="zscore">8.834300</data> <data key="promoter">chr12:77459306..77459365,-</data> </edge> <edge id="e75" source="E2F4" target="TFDP1"> <data key="zscore">12.764142</data> <data key="promoter">chr13:114238997..114239077,+</data> </edge> <edge id="e76" source="E2F4" target="ZNF828"> <data key="zscore">13.732920</data> <data key="promoter">chr13:115079949..115080022,+</data> </edge> <edge id="e77" source="E2F4" target="CTCF"> <data key="zscore">10.989668</data> <data key="promoter">chr16:67596417..67596497,+</data> </edge> <edge id="e78" source="E2F4" target="HOXB7"> <data key="zscore">5.976186</data> <data key="promoter">chr17:46687959..46688007,-</data> </edge> <edge id="e79" source="E2F4" target="DNMT1"> <data key="zscore">14.442942</data> <data key="promoter">chr19:10305581..10305646,-</data> </edge> <edge id="e80" source="E2F4" target="ZNF473"> <data 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<data key="zscore">6.980334</data> <data key="promoter">chr3:141868357..141868393,-</data> </edge> <edge id="e88" source="E2F4" target="MATR3"> <data key="zscore">5.335442</data> <data key="promoter">chr5:138629349..138629386,+</data> </edge> <edge id="e89" source="E2F4" target="MATR3"> <data key="zscore">9.145348</data> <data key="promoter">chr5:138629417..138629446,+</data> </edge> <edge id="e90" source="E2F4" target="E2F3"> <data key="zscore">11.747304</data> <data key="promoter">chr6:20402102..20402152,+</data> </edge> <edge id="e91" source="E2F4" target="SOX4"> <data key="zscore">5.461751</data> <data key="promoter">chr6:21593973..21593988,+</data> </edge> <edge id="e92" source="E2F4" target="TCF19"> <data key="zscore">11.251513</data> <data key="promoter">chr6:31126291..31126399,+</data> </edge> <edge id="e93" source="E2F4" target="GRHL2"> <data key="zscore">3.270715</data> <data key="promoter">chr8:102504651..102504683,+</data> </edge> <edge id="e94" source="E2F4" 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key="promoter">chr6:170863423..170863484,+</data> </edge> <edge id="e500" source="TFDP1" target="E2F3"> <data key="zscore">4.181640</data> <data key="promoter">chr6:20402102..20402152,+</data> </edge> <edge id="e501" source="TFDP1" target="TCF19"> <data key="zscore">3.912595</data> <data key="promoter">chr6:31126291..31126399,+</data> </edge> <edge id="e502" source="TFDP1" target="DNAJC2"> <data key="zscore">2.885620</data> <data key="promoter">chr7:102985160..102985273,-</data> </edge> <edge id="e503" source="TFDP1" target="GTF2I"> <data key="zscore">5.249992</data> <data key="promoter">chr7:74072021..74072119,+</data> </edge> <edge id="e504" source="TFDP1" target="PHTF2"> <data key="zscore">4.217160</data> <data key="promoter">chr7:77428149..77428220,+</data> </edge> <edge id="e505" source="TFDP1" target="ZFPM2"> <data key="zscore">2.314781</data> <data key="promoter">chr8:106330656..106330684,+</data> </edge> <edge id="e506" source="TFDP1" target="ZNF623"> <data key="zscore">5.252320</data> <data key="promoter">chr8:144718171..144718244,+</data> </edge> <edge id="e507" source="TFDP1" target="SMARCA1"> <data key="zscore">2.836590</data> <data key="promoter">chrX:128657457..128657475,-</data> </edge> <edge id="e508" source="TFDP1" target="ATRX"> <data key="zscore">2.769957</data> <data key="promoter">chrX:77041685..77041716,-</data> </edge> <edge id="e509" source="TFE3" target="NFIX"> <data key="zscore">2.512098</data> <data key="promoter">chr19:13106214..13106382,+</data> </edge> <edge id="e510" source="TFE3" target="ZNF507"> <data key="zscore">4.290077</data> <data key="promoter">chr19:32836499..32836551,+</data> </edge> <edge id="e511" source="TFE3" target="ZNF593"> <data key="zscore">6.795832</data> <data key="promoter">chr1:26496382..26496457,+</data> </edge> <edge id="e512" source="TFE3" target="LYAR"> <data key="zscore">3.218736</data> <data key="promoter">chr4:4291861..4291913,-</data> </edge> <edge id="e513" source="TFE3" target="MATR3"> <data key="zscore">5.344587</data> <data key="promoter">chr5:138609782..138609826,+</data> </edge> <edge id="e514" source="TFE3" target="PLAGL1"> <data key="zscore">1.795280</data> <data key="promoter">chr6:144329384..144329405,-</data> </edge> <edge id="e515" source="TFE3" target="FOXP4"> <data key="zscore">4.201205</data> <data key="promoter">chr6:41514078..41514158,+</data> </edge> <edge id="e516" source="TP53" target="NFKB2"> <data key="zscore">2.111995</data> <data key="promoter">chr10:104155455..104155479,+</data> </edge> <edge id="e517" source="TP53" target="FOSL1"> <data key="zscore">4.122302</data> <data key="promoter">chr11:65667846..65667868,-</data> </edge> <edge id="e518" source="TP53" target="FOSL1"> <data key="zscore">4.682434</data> <data key="promoter">chr11:65667884..65667895,-</data> </edge> <edge id="e519" source="TP53" target="ZNF219"> <data key="zscore">5.836272</data> <data key="promoter">chr14:21566731..21566836,-</data> </edge> <edge id="e520" source="TP53" target="ZNF580"> <data key="zscore">6.446524</data> <data key="promoter">chr19:56152361..56152434,+</data> </edge> <edge id="e521" source="TP53" target="MTA3"> <data key="zscore">5.386089</data> <data key="promoter">chr2:42795745..42795824,+</data> </edge> <edge id="e522" source="TP53" target="KCMF1"> <data key="zscore">5.878198</data> <data key="promoter">chr2:85198369..85198483,+</data> </edge> <edge id="e523" source="TP53" target="HMGXB3"> <data key="zscore">5.859824</data> <data key="promoter">chr5:149380256..149380343,+</data> </edge> <edge id="e524" source="TP53" target="SOX7"> <data key="zscore">3.651812</data> <data key="promoter">chr8:10588010..10588030,-</data> </edge> <edge id="e525" source="TP53" target="ZFHX4"> <data key="zscore">3.295039</data> <data key="promoter">chr8:77593474..77593612,+</data> </edge> <edge id="e526" source="ZHX3" target="EHF"> <data key="zscore">1.855803</data> <data key="promoter">chr11:34642612..34642646,+</data> </edge> <edge id="e527" source="ZHX3" target="EHF"> <data key="zscore">2.728882</data> <data key="promoter">chr11:34642656..34642667,+</data> </edge> <edge id="e528" source="ZHX3" target="SIX2"> <data key="zscore">1.689851</data> <data key="promoter">chr2:45236540..45236577,-</data> </edge> <edge id="e529" source="ZHX3" target="ZFHX4"> <data key="zscore">2.786958</data> <data key="promoter">chr8:77593474..77593612,+</data> </edge> <edge id="e530" source="ZNF143" target="ZNF37A"> <data key="zscore">5.641238</data> <data key="promoter">chr10:38383255..38383324,+</data> </edge> <edge id="e531" source="ZNF143" target="TFAM"> <data key="zscore">5.990048</data> <data key="promoter">chr10:60145155..60145206,+</data> </edge> <edge id="e532" source="ZNF143" target="ZBTB44"> <data key="zscore">1.993314</data> <data key="promoter">chr11:130184753..130184824,-</data> </edge> <edge id="e533" source="ZNF143" target="E2F8"> <data key="zscore">5.692288</data> <data key="promoter">chr11:19262421..19262455,-</data> </edge> <edge id="e534" source="ZNF143" target="ZNF605"> <data key="zscore">6.351872</data> <data key="promoter">chr12:133532864..133532899,-</data> </edge> <edge id="e535" source="ZNF143" target="ZNF268"> <data key="zscore">5.534235</data> <data key="promoter">chr12:133758072..133758114,+</data> </edge> <edge id="e536" source="ZNF143" target="FOXM1"> <data key="zscore">4.500617</data> <data key="promoter">chr12:2986206..2986258,-</data> </edge> <edge id="e537" source="ZNF143" target="FOXM1"> <data key="zscore">4.286797</data> <data key="promoter">chr12:2986275..2986363,-</data> </edge> <edge id="e538" source="ZNF143" target="ZNF828"> <data key="zscore">8.320008</data> <data key="promoter">chr13:115079949..115080022,+</data> </edge> <edge id="e539" source="ZNF143" target="ZNF280D"> <data key="zscore">4.043317</data> <data key="promoter">chr15:57025675..57025718,-</data> </edge> <edge id="e540" source="ZNF143" target="CTCF"> <data key="zscore">5.557490</data> <data key="promoter">chr16:67596417..67596497,+</data> </edge> <edge id="e541" source="ZNF143" target="MYST2"> <data key="zscore">3.204059</data> <data key="promoter">chr17:47866034..47866060,+</data> </edge> <edge id="e542" source="ZNF143" target="UNK"> <data key="zscore">6.414470</data> <data key="promoter">chr17:73780879..73780963,+</data> </edge> <edge id="e543" source="ZNF143" target="SOX15"> <data key="zscore">1.657774</data> <data key="promoter">chr17:7493405..7493419,-</data> </edge> <edge id="e544" source="ZNF143" target="TP53"> <data key="zscore">3.153098</data> <data key="promoter">chr17:7590797..7590815,-</data> </edge> <edge id="e545" source="ZNF143" target="DNMT1"> <data key="zscore">6.589135</data> <data key="promoter">chr19:10305581..10305646,-</data> </edge> <edge id="e546" source="ZNF143" target="MLL4"> <data key="zscore">2.478568</data> <data key="promoter">chr19:36208877..36208919,+</data> </edge> <edge id="e547" source="ZNF143" target="PPP1R13L"> <data key="zscore">2.716506</data> <data key="promoter">chr19:45908292..45908374,-</data> </edge> <edge id="e548" source="ZNF143" target="ZNF473"> <data key="zscore">7.899083</data> <data key="promoter">chr19:50529247..50529296,+</data> </edge> <edge id="e549" source="ZNF143" target="ZNF460"> <data key="zscore">1.605576</data> <data key="promoter">chr19:57791806..57791875,+</data> </edge> <edge id="e550" source="ZNF143" target="ZNF544"> <data key="zscore">6.713557</data> <data key="promoter">chr19:58740266..58740297,+</data> </edge> <edge id="e551" source="ZNF143" target="ZNF8"> <data key="zscore">7.286126</data> <data key="promoter">chr19:58790314..58790358,+</data> </edge> <edge id="e552" source="ZNF143" target="ZSCAN22"> <data key="zscore">6.041168</data> <data key="promoter">chr19:58838369..58838439,+</data> </edge> <edge id="e553" source="ZNF143" target="ZNF584"> <data key="zscore">6.831995</data> <data key="promoter">chr19:58920000..58920057,+</data> </edge> <edge id="e554" source="ZNF143" target="ZNF324"> <data key="zscore">3.288172</data> <data key="promoter">chr19:58978418..58978456,+</data> </edge> <edge id="e555" source="ZNF143" target="ZNF358"> <data key="zscore">2.891525</data> <data key="promoter">chr19:7580944..7581031,+</data> </edge> <edge id="e556" source="ZNF143" target="ZC3H15"> <data key="zscore">3.959290</data> <data key="promoter">chr2:187350973..187351072,+</data> </edge> <edge id="e557" source="ZNF143" target="CREB1"> <data key="zscore">3.650453</data> <data key="promoter">chr2:208394658..208394692,+</data> </edge> <edge id="e558" source="ZNF143" target="MYNN"> <data key="zscore">2.470315</data> <data key="promoter">chr3:169491171..169491205,+</data> </edge> <edge id="e559" source="ZNF143" target="NFXL1"> <data key="zscore">6.010468</data> <data key="promoter">chr4:47916588..47916607,-</data> </edge> <edge id="e560" source="ZNF143" target="PITX1"> <data key="zscore">3.023254</data> <data key="promoter">chr5:134369905..134369972,-</data> </edge> <edge id="e561" source="ZNF143" target="MATR3"> <data key="zscore">3.436943</data> <data key="promoter">chr5:138629349..138629386,+</data> </edge> <edge id="e562" source="ZNF143" target="MATR3"> <data key="zscore">4.788216</data> <data key="promoter">chr5:138629417..138629446,+</data> </edge> <edge id="e563" source="ZNF143" target="HMGXB3"> <data key="zscore">4.129164</data> <data key="promoter">chr5:149380256..149380343,+</data> </edge> <edge id="e564" source="ZNF143" target="TFAP2A"> <data key="zscore">2.476260</data> <data key="promoter">chr6:10419768..10419819,-</data> </edge> <edge id="e565" source="ZNF143" target="RXRB"> <data key="zscore">6.106647</data> <data key="promoter">chr6:33168126..33168180,-</data> </edge> <edge id="e566" source="ZNF143" target="ZNF451"> <data key="zscore">3.848880</data> <data key="promoter">chr6:56954919..56955000,+</data> </edge> <edge id="e567" source="ZNF143" target="NFE2L3"> <data key="zscore">1.954109</data> <data key="promoter">chr7:26191809..26191890,+</data> </edge> <edge id="e568" source="ZNF143" target="RBAK"> <data key="zscore">5.281784</data> <data key="promoter">chr7:5085480..5085510,+</data> </edge> <edge id="e569" source="ZNF143" target="ZNF12"> <data key="zscore">2.212581</data> <data key="promoter">chr7:6746529..6746591,-</data> </edge> <edge id="e570" source="ZNF143" target="GTF2I"> <data key="zscore">7.341711</data> <data key="promoter">chr7:74072021..74072119,+</data> </edge> <edge id="e571" source="ZNF143" target="NFKBIL2"> <data key="zscore">5.455692</data> <data key="promoter">chr8:145669791..145669834,-</data> </edge> <node id="MLX"> <data key="motif"></data> </node> <node id="ZFP64"> <data key="motif"></data> </node> <node id="YBX1"> <data key="motif"></data> </node> <node id="YY1"> <data key="motif"></data> </node> <node id="ZNF766"> <data key="motif"></data> </node> <node id="E2F8"> <data key="motif"></data> </node> <node id="ZNF326"> <data key="motif"></data> </node> <node id="CARHSP1"> <data key="motif"></data> </node> <node id="ZNF143"> <data key="motif">ZNF143</data> </node> <node id="ENO1"> <data key="motif"></data> </node> <node id="ZHX3"> <data key="motif">ADNP_IRX_SIX_ZHX</data> </node> <node id="ZNF142"> <data key="motif"></data> </node> <node id="PHF5A"> <data key="motif"></data> </node> <node id="ZNF263"> <data key="motif"></data> </node> <node id="NPAS2"> <data key="motif">bHLH_family</data> </node> <node id="NFYC"> <data key="motif">NFY{A,B,C}</data> </node> <node id="ATRX"> <data key="motif"></data> </node> <node id="ZNF823"> <data key="motif"></data> </node> <node id="TERF1"> <data key="motif"></data> </node> <node id="CREB3L2"> <data key="motif"></data> </node> <node id="FOXP4"> <data key="motif"></data> </node> <node id="ZNF37A"> <data key="motif"></data> </node> <node id="ZNF8"> <data key="motif"></data> </node> <node id="SOX7"> <data key="motif"></data> </node> <node id="ZNF385A"> <data key="motif"></data> </node> <node id="POU2F3"> <data key="motif">POU2F1..3</data> </node> <node id="FOXF2"> <data key="motif"></data> </node> <node id="NFKB2"> <data key="motif"></data> </node> <node id="NFE2L3"> <data key="motif"></data> </node> <node id="CDC5L"> <data key="motif">CDC5L</data> </node> <node id="CAMTA1"> <data key="motif"></data> </node> <node id="TEAD3"> <data key="motif"></data> </node> <node id="ZNF324"> <data key="motif"></data> </node> <node id="DBP"> <data key="motif"></data> </node> <node id="ZFPM2"> <data key="motif"></data> </node> <node id="MYST2"> <data key="motif"></data> </node> <node id="EHF"> <data key="motif"></data> </node> <node id="PPP1R13L"> <data key="motif"></data> </node> <node id="TP53"> <data key="motif">TP53</data> </node> <node id="HES4"> <data key="motif"></data> </node> <node id="ZNF605"> <data key="motif"></data> </node> <node id="PITX1"> <data key="motif"></data> </node> <node id="MTA2"> <data key="motif"></data> </node> <node id="ZFHX4"> <data key="motif"></data> </node> <node id="ID1"> <data key="motif">bHLH_family</data> </node> <node id="MNT"> <data key="motif">bHLH_family</data> </node> <node id="ZNF12"> <data key="motif"></data> </node> <node id="JDP2"> <data key="motif"></data> </node> <node id="TFAP2C"> <data key="motif"></data> </node> <node id="JUND"> <data key="motif"></data> </node> <node id="ZNF544"> <data key="motif"></data> </node> <node id="POU2F1"> <data key="motif">POU2F1..3</data> </node> <node id="HMGXB3"> <data key="motif"></data> </node> <node id="ZC3H15"> <data key="motif"></data> </node> <node id="ZNF628"> <data key="motif"></data> </node> <node id="MATR3"> <data key="motif"></data> </node> <node id="TBP"> <data key="motif"></data> </node> <node id="ELF3"> <data key="motif"></data> </node> <node id="ZNF460"> <data key="motif"></data> </node> <node id="ZNF473"> <data key="motif"></data> </node> <node id="PRKRIR"> <data key="motif"></data> </node> <node id="SREBF2"> <data key="motif"></data> </node> <node id="ZCCHC11"> <data key="motif"></data> </node> <node id="CREBZF"> <data key="motif"></data> </node> <node id="CIZ1"> <data key="motif"></data> </node> <node id="ADNP2"> <data key="motif"></data> </node> <node id="HLTF"> <data key="motif"></data> </node> <node id="PCBP1"> <data key="motif"></data> </node> <node id="TFDP2"> <data key="motif"></data> </node> <node id="DNAJC2"> <data key="motif"></data> </node> <node id="HMG20B"> <data key="motif"></data> </node> <node id="FOXQ1"> <data key="motif">FOXQ1</data> </node> <node id="ZBTB11"> <data key="motif"></data> </node> <node id="GATAD2B"> <data key="motif"></data> </node> <node id="HMGA1"> <data key="motif"></data> </node> <node id="ZNF512B"> <data key="motif"></data> </node> <node id="ZNF580"> <data key="motif"></data> </node> <node id="ZSCAN22"> <data key="motif"></data> </node> <node id="HOXB7"> <data key="motif"></data> </node> <node id="PAWR"> <data key="motif"></data> </node> <node id="LYAR"> <data key="motif"></data> </node> <node id="MYC"> <data 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</node> <node id="tf_MYC"> <data key="type">tf</data> <data key="label">MYC</data> </node> <node id="tf_GTF2I"> <data key="type">tf</data> <data key="label">GTF2I</data> </node> <node id="tf_ESRRA"> <data key="type">tf</data> <data key="label">ESRRA</data> </node> <node id="tf_IRF3"> <data key="type">tf</data> <data key="label">IRF3</data> </node> <node id="tf_HOXA1"> <data key="type">tf</data> <data key="label">HOXA1</data> </node> <node id="tf_SOX4"> <data key="type">tf</data> <data key="label">SOX4</data> </node> <node id="tf_CEBPG"> <data key="type">tf</data> <data key="label">CEBPG</data> </node> <node id="tf_E2F1"> <data key="type">tf</data> <data key="label">E2F1</data> </node> <node id="tf_THAP1"> <data key="type">tf</data> <data key="label">THAP1</data> </node> <node id="tf_NCOR1"> <data key="type">tf</data> <data key="label">NCOR1</data> </node> <node id="tf_TFAM"> <data key="type">tf</data> <data key="label">TFAM</data> </node> <node id="tf_ZNF584"> <data key="type">tf</data> <data key="label">ZNF584</data> </node> <node id="tf_SOX15"> <data key="type">tf</data> <data key="label">SOX15</data> </node> <node id="tf_SIX2"> <data key="type">tf</data> <data key="label">SIX2</data> </node> <node id="tf_GATAD2A"> <data key="type">tf</data> <data key="label">GATAD2A</data> </node> <node id="tf_TFE3"> <data key="type">tf</data> <data key="label">TFE3</data> </node> <node id="tf_ZNF687"> <data key="type">tf</data> <data key="label">ZNF687</data> </node> <node id="tf_TEAD1"> <data key="type">tf</data> <data key="label">TEAD1</data> </node> <node id="tf_SP2"> <data key="type">tf</data> <data key="label">SP2</data> </node> <node id="tf_ETV5"> <data key="type">tf</data> <data key="label">ETV5</data> </node> <node id="tf_SNAI2"> <data key="type">tf</data> <data key="label">SNAI2</data> </node> <node id="tf_MLL4"> <data key="type">tf</data> <data key="label">MLL4</data> </node> <node id="tf_NONO"> <data key="type">tf</data> <data key="label">NONO</data> </node> <node id="tf_ZNF726"> <data key="type">tf</data> <data key="label">ZNF726</data> </node> <node id="tf_NFE2L1"> <data key="type">tf</data> <data key="label">NFE2L1</data> </node> <node id="tf_MLLT1"> <data key="type">tf</data> <data key="label">MLLT1</data> </node> <node id="tf_ZNF219"> <data key="type">tf</data> <data key="label">ZNF219</data> </node> <node id="tf_UNK"> <data key="type">tf</data> <data key="label">UNK</data> </node> <node id="tf_SFPQ"> <data key="type">tf</data> <data key="label">SFPQ</data> </node> <node id="tf_E2F7"> <data key="type">tf</data> <data key="label">E2F7</data> </node> <node id="tf_BRCA1"> <data key="type">tf</data> <data key="label">BRCA1</data> </node> <node id="tf_E2F3"> <data key="type">tf</data> <data key="label">E2F3</data> </node> <node id="tf_GATA2"> <data key="type">tf</data> <data key="label">GATA2</data> </node> <node id="tf_ELK1"> <data key="type">tf</data> <data key="label">ELK1</data> </node> <node id="tf_PHTF2"> <data key="type">tf</data> <data key="label">PHTF2</data> </node> <node id="tf_LASS6"> <data key="type">tf</data> <data key="label">LASS6</data> </node> <node id="tf_MECP2"> <data key="type">tf</data> <data key="label">MECP2</data> </node> <node id="tf_HOXB6"> <data key="type">tf</data> <data key="label">HOXB6</data> </node> <node id="tf_ZNF623"> <data key="type">tf</data> <data key="label">ZNF623</data> </node> <node id="tf_MYNN"> <data key="type">tf</data> <data key="label">MYNN</data> </node> <node id="tf_AEBP2"> <data key="type">tf</data> <data key="label">AEBP2</data> </node> <node id="tf_MXD3"> <data key="type">tf</data> <data key="label">MXD3</data> </node> <node id="tf_ETV4"> <data key="type">tf</data> <data key="label">ETV4</data> </node> <node id="tf_CSDA"> <data key="type">tf</data> <data key="label">CSDA</data> </node> <node id="tf_CTCF"> <data key="type">tf</data> <data key="label">CTCF</data> </node> <node id="tf_FOSL1"> <data key="type">tf</data> <data key="label">FOSL1</data> </node> <node id="tf_MTA3"> <data key="type">tf</data> <data key="label">MTA3</data> </node> <node id="tf_KCMF1"> <data key="type">tf</data> <data key="label">KCMF1</data> </node> <node id="tf_FOXK2"> <data key="type">tf</data> <data key="label">FOXK2</data> </node> <node id="tf_RBAK"> <data key="type">tf</data> <data key="label">RBAK</data> </node> <node id="tf_NFYB"> <data key="type">tf</data> <data key="label">NFYB</data> </node> <node id="tf_DNMT1"> <data key="type">tf</data> <data key="label">DNMT1</data> </node> <node id="tf_HES1"> <data key="type">tf</data> <data key="label">HES1</data> </node> <node id="tf_SRF"> <data key="type">tf</data> <data key="label">SRF</data> </node> <node id="tf_MAZ"> <data key="type">tf</data> <data key="label">MAZ</data> </node> <node id="tf_ZNF593"> <data key="type">tf</data> <data key="label">ZNF593</data> </node> <node id="tf_HMGXB4"> <data key="type">tf</data> <data key="label">HMGXB4</data> </node> <node id="tf_ZNF296"> <data key="type">tf</data> <data key="label">ZNF296</data> </node> <node id="tf_HIST2H2AC"> <data key="type">tf</data> <data key="label">HIST2H2AC</data> </node> <node id="tf_NFIX"> <data key="type">tf</data> <data key="label">NFIX</data> </node> <node id="tf_RUNX1"> <data key="type">tf</data> <data key="label">RUNX1</data> </node> <node id="tf_ZNF629"> <data key="type">tf</data> <data key="label">ZNF629</data> </node> <node id="tf_PAX6"> <data key="type">tf</data> <data key="label">PAX6</data> </node> <node id="tf_DLX2"> <data key="type">tf</data> <data key="label">DLX2</data> </node> <node id="tf_NFXL1"> <data key="type">tf</data> <data key="label">NFXL1</data> </node> <node id="tf_TP63"> <data key="type">tf</data> <data key="label">TP63</data> </node> <node id="tf_DDB2"> <data key="type">tf</data> <data key="label">DDB2</data> </node> <node id="tf_TBX20"> <data key="type">tf</data> <data key="label">TBX20</data> </node> <node id="tf_TCF19"> <data key="type">tf</data> <data key="label">TCF19</data> </node> <node id="tf_ZNF358"> <data key="type">tf</data> <data key="label">ZNF358</data> </node> <node id="tf_HSF1"> <data key="type">tf</data> <data key="label">HSF1</data> </node> <node id="tf_C14ORF106"> <data key="type">tf</data> <data key="label">C14ORF106</data> </node> <node id="tf_GMEB2"> <data key="type">tf</data> <data key="label">GMEB2</data> </node> <node id="tf_ZNF280D"> <data key="type">tf</data> <data key="label">ZNF280D</data> </node> <node id="tf_TEF"> <data key="type">tf</data> <data key="label">TEF</data> </node> <node id="tf_FUBP1"> <data key="type">tf</data> <data key="label">FUBP1</data> </node> <node id="tf_NFYA"> <data key="type">tf</data> <data key="label">NFYA</data> </node> <node id="tf_SMARCA1"> <data key="type">tf</data> <data key="label">SMARCA1</data> </node> <node id="tf_STIL"> <data key="type">tf</data> <data key="label">STIL</data> </node> <node id="tf_HNRNPK"> <data key="type">tf</data> <data key="label">HNRNPK</data> </node> <node id="tf_ELF1"> <data key="type">tf</data> <data key="label">ELF1</data> </node> <node id="tf_TOX2"> <data key="type">tf</data> <data key="label">TOX2</data> </node> <node id="tf_GRHL2"> <data key="type">tf</data> <data key="label">GRHL2</data> </node> <node id="tf_ZBTB44"> <data key="type">tf</data> <data key="label">ZBTB44</data> </node> <node id="tf_NR2F2"> <data key="type">tf</data> <data key="label">NR2F2</data> </node> <node id="tf_TFDP1"> <data key="type">tf</data> <data key="label">TFDP1</data> </node> <node id="tf_ZNF268"> <data key="type">tf</data> <data key="label">ZNF268</data> </node> <node id="tf_TFAP2A"> <data key="type">tf</data> <data key="label">TFAP2A</data> </node> <node id="tf_PBX1"> <data key="type">tf</data> <data key="label">PBX1</data> </node> <node id="tf_TFAP4"> <data key="type">tf</data> <data key="label">TFAP4</data> </node> <node id="tf_MXI1"> <data key="type">tf</data> <data key="label">MXI1</data> </node> <node id="tf_TEAD4"> <data key="type">tf</data> <data key="label">TEAD4</data> </node> <node id="tf_ERF"> <data key="type">tf</data> <data key="label">ERF</data> </node> <node id="tf_BBX"> <data key="type">tf</data> <data key="label">BBX</data> </node> <node id="tf_ZNF644"> <data key="type">tf</data> <data key="label">ZNF644</data> </node> <node id="tf_RBPJ"> <data key="type">tf</data> <data key="label">RBPJ</data> </node> <node id="tf_ZNF507"> <data key="type">tf</data> <data key="label">ZNF507</data> </node> <node id="tf_FOXM1"> <data key="type">tf</data> <data key="label">FOXM1</data> </node> <node id="tf_PLAGL1"> <data key="type">tf</data> <data key="label">PLAGL1</data> </node> <node id="tf_BNC1"> <data key="type">tf</data> <data key="label">BNC1</data> </node> <node id="tf_ADNP"> <data key="type">tf</data> <data key="label">ADNP</data> </node> <node id="tf_ZNF26"> <data key="type">tf</data> <data key="label">ZNF26</data> </node> <node id="tf_ANKZF1"> <data key="type">tf</data> <data key="label">ANKZF1</data> </node> <node id="tf_NFKBIL2"> <data key="type">tf</data> <data key="label">NFKBIL2</data> </node> <node id="tf_ZNF451"> <data key="type">tf</data> <data key="label">ZNF451</data> </node> <node id="tf_E2F4"> <data key="type">tf</data> <data key="label">E2F4</data> </node> <node id="tf_FOXA1"> <data key="type">tf</data> <data key="label">FOXA1</data> </node> <node id="tf_GON4L"> <data key="type">tf</data> <data key="label">GON4L</data> </node> <node id="tf_ZNF828"> <data key="type">tf</data> <data key="label">ZNF828</data> </node> <node id="tf_BCL11A"> <data key="type">tf</data> <data key="label">BCL11A</data> </node> <node id="tf_CREB1"> <data key="type">tf</data> <data key="label">CREB1</data> </node> <node id="tf_ARNTL2"> <data key="type">tf</data> <data key="label">ARNTL2</data> </node> <node id="tf_RXRB"> <data key="type">tf</data> <data key="label">RXRB</data> </node> <node id="motif_ADNP_IRX_SIX_ZHX"> <data key="type">motif</data> <data key="label">ADNP_IRX_SIX_ZHX</data> </node> <node id="motif_TEF"> <data key="type">motif</data> <data key="label">TEF</data> </node> <node id="motif_FOXQ1"> <data key="type">motif</data> <data key="label">FOXQ1</data> </node> <node id="motif_TEAD1"> <data key="type">motif</data> <data key="label">TEAD1</data> </node> <node id="motif_SNAI1..3"> <data key="type">motif</data> <data key="label">SNAI1..3</data> </node> <node id="motif_NFY{A,B,C}"> <data key="type">motif</data> <data key="label">NFY{A,B,C}</data> </node> <node id="motif_E2F1..5"> <data key="type">motif</data> <data key="label">E2F1..5</data> </node> <node id="motif_CDC5L"> <data key="type">motif</data> <data key="label">CDC5L</data> </node> <node id="motif_RBPJ"> <data key="type">motif</data> <data key="label">RBPJ</data> </node> <node id="motif_bHLH_family"> <data key="type">motif</data> <data key="label">bHLH_family</data> </node> <node id="motif_POU2F1..3"> <data key="type">motif</data> <data key="label">POU2F1..3</data> </node> <node id="motif_TFDP1"> <data key="type">motif</data> <data key="label">TFDP1</data> </node> <node id="motif_ZNF143"> <data key="type">motif</data> <data key="label">ZNF143</data> </node> <node id="motif_TP53"> <data key="type">motif</data> <data key="label">TP53</data> </node> </graph> </graphml>'; | |||
var z_min = 0; | var z_min = 0; | ||
var z_max = 1; | var z_max = 1; | ||
var edge_type = ""; | |||
var t; | var t; | ||
var selected = false; | var selected = false; | ||
function sliderTrack() { | |||
z_min = $('#slider1').noUiSlider('getValue', {point: 'lower'}); | |||
z_max = $('#slider1').noUiSlider('getValue', {point: 'upper'}); | |||
z_min = Math.round(z_min*100)/100; | |||
z_max = Math.round(z_max*100)/100; | |||
$("#cyto_zscore_filter_min").val(z_min); | |||
$("#cyto_zscore_filter_max").val(z_max); | |||
//clearTimeout(t); | |||
//t = setTimeout("setScoreFilter()", 100); | |||
} | |||
function sliderChange() { | |||
sliderTrack(); | |||
setScoreFilter(); | |||
} | |||
function setScoreFilter() { | |||
vis.filter("edges", function(edge) { | |||
return (((edge.data.zscore >= z_min)&&(edge.data.zscore <= z_max)) || (!edge.data.zscore)); | |||
}, true); | |||
} | |||
function setEdgeFilter(type) { | |||
edge_type = type; | |||
vis.filter("edges", function(edge) { | |||
return ((edge_type == "") || (edge.data.type == edge_type)); | |||
}, true); | |||
} | |||
function graphClick(event) { | function graphClick(event) { | ||
var target = event.target; | var target = event.target; | ||
var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data[" | var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data["id"]; | ||
window.location = lurl; | //window.location = lurl; | ||
//alert( | alert(lurl); | ||
} | |||
function nodeClick(event) { | |||
var target = event.target; | |||
//alert(target.data["id"]); | |||
//selectFirstNeighbors(target.data["id"]); | |||
var fn = vis.firstNeighbors([target.data["id"]]); | |||
var nodes = fn.neighbors.concat(fn.rootNodes); | |||
vis.deselect(); | |||
vis.select(nodes); | |||
alert(nodes.length); | |||
} | } | ||
function graphSelect() { | function graphSelect() { | ||
var edges = vis.selected("edges"); | var edges = vis.selected("edges"); | ||
var nodes = vis.selected("nodes"); | var nodes = vis.selected("nodes"); | ||
//var container = document.getElementById("TF_list"); | |||
if (edges.length == 0 && nodes.length == 1) { | |||
selectFirstNeighbors(nodes[0]); | |||
return; | |||
} | |||
var html = "<tr><th>node</th><th>type</th></tr>"; | |||
//var sel = vis.selected(); | |||
for (var i in nodes) { | |||
var data = nodes[i].data; | |||
html += "<tr><td>"+data.label+"</td><td>"+data.type+"</td></tr>"; | |||
//selectFirstNeighbors(nodes[i]); | |||
} | |||
//($("#nodes_list").innerHTML); | |||
$("#nodes_list").html(html); | |||
html = "<tr><th>Source TF</th><th>Target TF</th><th>Promoter</th><th>Z-Score</th></tr>"; | |||
//var sel = vis.selected(); | |||
for (var i in edges) { | |||
var data = edges[i].data; | |||
html += "<tr><td>"+data.source+"</td><td>"+data.target+"</td><td>"+(data.promoter ? data.promoter : "na")+"</td><td>"+(data.zscore ? data.zscore : "na")+"</td></tr>"; | |||
} | |||
$("#edges_list").html(html); | |||
selected = ((edges.length > 0) || (nodes.length > 0)); | selected = ((edges.length > 0) || (nodes.length > 0)); | ||
vis.visualStyle(visual_style); | vis.visualStyle(visual_style); | ||
//if ((edges.length > 0) && (nodes.length > 0)) { | |||
// selected = true; | |||
//} | |||
} | |||
function layoutChange() { | |||
vis.layout($("#cyto_layout").val()); | |||
} | |||
function highlightFirstNeighbors(target) { | |||
setTimeout(function() { | |||
if (_mouseOverNode != null && _mouseOverNode.data.id === target.data.id) { | |||
var fn = vis.firstNeighbors([target]); | |||
var bypass = { nodes: {}, edges: {} }; | |||
var allNodes = vis.nodes(); | |||
jQuery.each(allNodes, function(i, n) { | |||
bypass.nodes[n.data.id] = { opacity: 0.2 }; | |||
}); | |||
var neighbors = fn.neighbors; | |||
neighbors = neighbors.concat(fn.rootNodes); | |||
jQuery.each(neighbors, function(i, n) { | |||
if (n.data.label.substr(0,3) == "miR"){ | |||
bypass.nodes[n.data.id] = {opacity: 1, labelFontSize: 11, labelVerticalAnchor: "bottom", label: n.data.label.substr(0,3)+"\n"+n.data.label.substr(3,n.data.label.length)}; | |||
} else { | |||
bypass.nodes[n.data.id] = { opacity: 1 }; | |||
} | |||
}); | |||
var allEdges = vis.edges(); | |||
jQuery.each(allEdges, function(i, e) { | |||
bypass.edges[e.data.id] = { opacity: 0.1 }; | |||
}); | |||
var edges = fn.edges; | |||
jQuery.each(edges, function(i, e) { | |||
bypass.edges[e.data.id] = { opacity: 1, width: 2 }; | |||
}); | |||
if (target.data.label.substr(0,3) == "miR"){ | |||
bypass.nodes[target.data.id] = {labelFontSize: 11, labelVerticalAnchor: "bottom"}; | |||
} | |||
vis.visualStyleBypass(bypass); | |||
} | |||
}, 400); | |||
} | |||
function clearFirstNeighborsHighligh() { | |||
setTimeout(function() { | |||
if (_mouseOverNode == null) { | |||
vis.visualStyleBypass({}); | |||
} | |||
}, 400); | |||
} | |||
function selectFirstNeighbors(node) { | |||
var fn = vis.firstNeighbors([node]); | |||
var nodes = fn.neighbors.concat(fn.rootNodes); | |||
var edges = fn.edges; | |||
vis.deselect(); | |||
vis.select(nodes); | |||
vis.select(edges); | |||
} | |||
function exportNet(type) { //TODO | |||
if (type == "sif") { | |||
vis.exportNetwork(type, 'cytoscapeNetworkExport.do?type='+type, { interactionAttr: "label", nodeAttr: "label" }); | |||
} else { | |||
vis.exportNetwork(type, 'cytoscapeNetworkExport.do?type='+type); | |||
} | |||
} | } | ||
$("#cyto_layout").change(function(){ | |||
layoutChange(); | |||
return false; | |||
}); | |||
$("#cyto_recalc").click(function(){ | |||
layoutChange(); | |||
return false; | |||
}); | |||
$("#cyto_tf_motif_filter").click(function(){ | |||
setEdgeFilter("has_motif"); | |||
return false; | |||
}); | |||
$("#cyto_motif_tf_filter").click(function(){ | |||
setEdgeFilter("promotes"); | |||
return false; | |||
}); | |||
$("#cyto_all_filter").click(function(){ | |||
setEdgeFilter(""); | |||
return false; | |||
}); | |||
// id of Cytoscape Web container div | // id of Cytoscape Web container div | ||
| Line 139: | Line 313: | ||
borderColor: "#000000", | borderColor: "#000000", | ||
size: 30, | size: 30, | ||
//color: "# | //color: "#ffffff", | ||
color: { defaultValue: "#ff9900", discreteMapper: colorMapper }, | color: { defaultValue: "#ff9900", discreteMapper: colorMapper }, | ||
//opacity: 0.8, | //opacity: 0.8, | ||
| Line 145: | Line 319: | ||
selectionOpacity: 0.8, | selectionOpacity: 0.8, | ||
hoverOpacity: 0.8, | hoverOpacity: 0.8, | ||
labelHorizontalAnchor: "center" | labelHorizontalAnchor: "center", | ||
mass: 0 | |||
}, | }, | ||
edges: { | edges: { | ||
width: { | width: { passthroughMapper: { attrName: "zscore" } }, | ||
label: { passthroughMapper: { attrName: "promoter" } }, | label: { passthroughMapper: { attrName: "promoter" } }, | ||
//tooltipText: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}", | //tooltipText: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}", | ||
| Line 161: | Line 336: | ||
selectionOpacity: 0.8, | selectionOpacity: 0.8, | ||
hoverOpacity: 0.8, | hoverOpacity: 0.8, | ||
labelGlowColor: "#000000" | labelGlowColor: "#000000", | ||
weight: 50000 | |||
} | } | ||
}; | }; | ||
// initialization options | // initialization options | ||
var options = { | |||
swfPath: "swf/CytoscapeWeb", | |||
flashInstallerPath: "swf/playerProductInstall" | |||
//swfPath: "/resource_browser/rb_js/cytoscapeweb/swf/CytoscapeWeb", | |||
//flashInstallerPath: "/resource_browser/rb_js/cytoscapeweb/swf/playerProductInstall" | |||
}; | |||
var vis = new org.cytoscapeweb.Visualization(div_id, options); | var vis = new org.cytoscapeweb.Visualization(div_id, options); | ||
| Line 178: | Line 354: | ||
return (selected) ? 0.3 : 0.6; | return (selected) ? 0.3 : 0.6; | ||
}; | }; | ||
// callback when Cytoscape Web has finished drawing | // callback when Cytoscape Web has finished drawing | ||
vis.ready(function() { | vis.ready(function() { | ||
| Line 185: | Line 361: | ||
vis.addListener("dblclick", "nodes", graphClick) | vis.addListener("dblclick", "nodes", graphClick) | ||
.addListener("dblclick", "edges", graphClick) | .addListener("dblclick", "edges", graphClick) | ||
//.addListener("click", "nodes", nodeClick) | |||
.addListener("select", "", graphSelect) | .addListener("select", "", graphSelect) | ||
.addListener("deselect", "", graphSelect); | .addListener("deselect", "", graphSelect); | ||
var edges = vis.edges(); | |||
for (var i in edges) { | |||
var data = edges[i].data; | |||
if (z_max < data.zscore) { z_max = data.zscore; } | |||
} | |||
z_max = Math.ceil(z_max); | |||
z_min = Math.floor(z_min); | |||
$(".sliderbar").noUiSlider("init", { scale: [z_min, z_max], startMin: z_min, startMax: z_max, tracker: sliderTrack, change: sliderChange }); | |||
$("#cyto_zscore_filter_min").val(z_min); | |||
$("#cyto_zscore_filter_max").val(z_max); | |||
$("#cyto_zscore_min").html(z_min); | |||
$("#cyto_zscore_max").html(z_max); | |||
graphSelect(); // Empty | |||
vis.filter("edges", function(edge) { | |||
return (edge.data.type = "promotes"); | |||
}, true); | |||
}); | }); | ||
var layoutOptions = { | |||
//gravitation: -500, | |||
autoStabilize: false, | |||
//maxTime: 240000, | |||
//weightAttr: "weight", | |||
//weightNorm: "log", | |||
//mass: 0 | |||
}; | |||
// draw options | // draw options | ||
| Line 197: | Line 405: | ||
nodeTooltipsEnabled: true, | nodeTooltipsEnabled: true, | ||
edgeTooltipsEnabled: true, | edgeTooltipsEnabled: true, | ||
layout: { name: "ForceDirected", options: layoutOptions }, | |||
// hide pan zoom | // hide pan zoom | ||
panZoomControlVisible: true | panZoomControlVisible: true | ||
Revision as of 13:19, 8 May 2012
FF:10717-109I6, TF to Motif to TF network
Mouseover nodes and edges to see attributes. Motifs are shown in orange, TFs are shown in blue. Promoter and z-score are attributes of the Motif to TF edges (blue arrow). TF to Motif edges are shown in orange.
Motifs shown are the top (maximum 30) motifs in the sample. TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample. Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).
Cytoscape Web will replace the contents of this div with your graph.
| TF | Motif |
|---|
| Source TF | Target TF | Promoter | Z-Score |
|---|
