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code.js
$(function(){ // on dom ready
var cy = cytoscape({
container: document.getElementById('cy'),
style: cytoscape.stylesheet()
.selector('node')
.css({
'font-size': 10,
'content': 'data(gene_name)',
'text-valign': 'center',
'color': 'white',
'text-outline-width': 2,
'text-outline-color': '#888',
'min-zoomed-font-size': 8,
'width': 'mapData(score, 0, 1, 20, 50)',
'height': 'mapData(score, 0, 1, 20, 50)'
})
.selector('node[node_type = "query"]')
.css({
'background-color': '#666',
'text-outline-color': '#666'
})
.selector('node:selected')
.css({
'background-color': '#000',
'text-outline-color': '#000'
})
.selector('edge')
.css({
'curve-style': 'haystack',
'opacity': 0.333,
'width': 'mapData(normalized_max_weight, 0, 0.01, 1, 2)'
})
.selector('edge[data_type = "Predicted"]')
.css({
'line-color': '#F6C28C'
})
.selector('edge[data_type = "Physical interactions"]')
.css({
'line-color': '#EAA2A3'
})
.selector('edge[data_type = "Shared protein domains"]')
.css({
'line-color': '#DAD4A8'
})
.selector('edge[data_type = "Co-expression"]')
.css({
'line-color': '#D0B7D3'
})
.selector('edge[data_type = "Pathway"]')
.css({
'line-color': '#9BD8DD'
})
.selector('edge[data_type = "Co-localization"]')
.css({
'line-color': '#A0B3D8'
})
.selector('edge:selected')
.css({
opacity: 1
}),
elements: cy3json.elements,
layout: {
name: 'concentric',
concentric: function(){
return this.data('score');
},
levelWidth: function(nodes){
return 0.5;
},
padding: 10
}
});
}); // on dom ready
// data exported from cytoscape desktop
var cy3json = {
"format_version" : "1.0",
"generated_by" : "cytoscape-3.1.0",
"target_cytoscapejs_version" : "~2.1",
"data" : {
"SUID" : 52,
"source_networks" : "[{\"group\":\"Predicted\",\"name\":\"I2D-BioGRID-Worm2Human\",\"weight\":3.7537451003449705E-4},{\"group\":\"Predicted\",\"name\":\"I2D-BIND-Yeast2Human\",\"weight\":0.06643631843947942},{\"group\":\"Co-localization\",\"name\":\"Schadt-Shoemaker-2004\",\"weight\":0.005333824227094584},{\"group\":\"Predicted\",\"name\":\"I2D-BioGRID-Fly2Human\",\"weight\":8.466550334425771E-4},{\"group\":\"Co-expression\",\"name\":\"Alizadeh-Staudt-2000\",\"weight\":0.013588094881204627},{\"group\":\"Pathway\",\"name\":\"PATHWAYCOMMONS-NCI_NATURE\",\"weight\":0.08635086720330279},{\"group\":\"Co-expression\",\"name\":\"Burington-Shaughnessy-2008\",\"weight\":0.03016969103761588},{\"group\":\"Physical interactions\",\"name\":\"BIOGRID-SMALL-SCALE-STUDIES\",\"weight\":0.030795064046860252},{\"group\":\"Co-expression\",\"name\":\"Perou-Botstein-2000\",\"weight\":2.4071521302299352E-4},{\"group\":\"Predicted\",\"name\":\"I2D-BIND-Worm2Human\",\"weight\":0.03170087557651741},{\"group\":\"Co-localization\",\"name\":\"Johnson-Shoemaker-2003\",\"weight\":0.03032705231517992},{\"group\":\"Predicted\",\"name\":\"I2D-IntAct-Worm2Human\",\"weight\":0.009475525484917712},{\"group\":\"Physical interactions\",\"name\":\"IREF-GRID\",\"weight\":0.05202868950330718},{\"group\":\"Physical interactions\",\"name\":\"IREF-BIND\",\"weight\":0.0034431917200112563},{\"group\":\"Predicted\",\"name\":\"I2D-BioGRID-Yeast2Human\",\"weight\":0.010253520175191107},{\"group\":\"Co-expression\",\"name\":\"Chen-Brown-2002\",\"weight\":0.008589403325972167},{\"group\":\"Physical interactions\",\"name\":\"IREF-SMALL-SCALE-STUDIES\",\"weight\":0.04307883818399897},{\"group\":\"Co-expression\",\"name\":\"Innocenti-Brown-2011\",\"weight\":3.737815236946745E-5},{\"group\":\"Co-expression\",\"name\":\"Rieger-Chu-2004\",\"weight\":0.010671838043867217},{\"group\":\"Co-expression\",\"name\":\"Wang-Maris-2006\",\"weight\":0.003589232071383274},{\"group\":\"Predicted\",\"name\":\"I2D-IntAct-Fly2Human\",\"weight\":0.0027282833691831326},{\"group\":\"Co-expression\",\"name\":\"Kang-Willman-2010\",\"weight\":0.006613416777023772},{\"group\":\"Predicted\",\"name\":\"I2D-IntAct-Mouse2Human\",\"weight\":0.03077726477940408},{\"group\":\"Co-expression\",\"name\":\"Arijs-Rutgeerts-2009\",\"weight\":0.008025541134347046},{\"group\":\"Co-expression\",\"name\":\"Roth-Zlotnik-2006\",\"weight\":2.3094160705350745E-4},{\"group\":\"Shared protein domains\",\"name\":\"PFAM\",\"weight\":0.10866564558714463},{\"group\":\"Predicted\",\"name\":\"I2D-Krogan-Greenblatt-2006-NonCore-Yeast2Human\",\"weight\":0.01808853933421063},{\"group\":\"Co-expression\",\"name\":\"Boldrick-Relman-2002\",\"weight\":0.012497804689359007},{\"group\":\"Predicted\",\"name\":\"I2D-vonMering-Bork-2002-High-Yeast2Human\",\"weight\":0.08260972953832166},{\"group\":\"Shared protein domains\",\"name\":\"INTERPRO\",\"weight\":0.037660450247227646},{\"group\":\"Predicted\",\"name\":\"I2D-Yu-Vidal-2008-GoldStd-Yeast2Human\",\"weight\":0.10890272340733954},{\"group\":\"Predicted\",\"name\":\"I2D-Krogan-Greenblatt-2006-Core-Yeast2Human\",\"weight\":0.09078863734632636},{\"group\":\"Predicted\",\"name\":\"I2D-BIND-Mouse2Human\",\"weight\":0.05507887303828558}]",
"type" : "genemania",
"attribute_search_limit" : 20,
"organism" : "H. sapiens",
"selected" : true,
"__Annotations" : [ ],
"name" : "H. sapiens (1)",
"combining_method" : "automatic",
"data_version" : "2013-10-15",
"annotations" : "[{\"name\":\"GO:0006310\",\"description\":\"DNA recombination\",\"qValue\":3.807166146987865E-40,\"sample\":23,\"total\":134},{\"name\":\"GO:0006281\",\"description\":\"DNA repair\",\"qValue\":2.9256714755984663E-30,\"sample\":22,\"total\":283},{\"name\":\"GO:0007131\",\"description\":\"reciprocal meiotic recombination\",\"qValue\":3.758570963819923E-26,\"sample\":13,\"total\":32},{\"name\":\"GO:0035825\",\"description\":\"reciprocal DNA recombination\",\"qValue\":3.758570963819923E-26,\"sample\":13,\"total\":32},{\"name\":\"GO:0051327\",\"description\":\"M phase of meiotic cell cycle\",\"qValue\":4.5961763932358935E-25,\"sample\":15,\"total\":81},{\"name\":\"GO:0007126\",\"description\":\"meiosis\",\"qValue\":4.5961763932358935E-25,\"sample\":15,\"total\":81},{\"name\":\"GO:0051321\",\"description\":\"meiotic cell cycle\",\"qValue\":4.817842748225099E-25,\"sample\":15,\"total\":82},{\"name\":\"GO:0007127\",\"description\":\"meiosis I\",\"qValue\":1.0294539910679028E-23,\"sample\":13,\"total\":48},{\"name\":\"GO:0043566\",\"description\":\"structure-specific DNA binding\",\"qValue\":8.73612488275016E-21,\"sample\":15,\"total\":154},{\"name\":\"GO:0008094\",\"description\":\"DNA-dependent ATPase activity\",\"qValue\":6.242716316472329E-18,\"sample\":11,\"total\":56},{\"name\":\"GO:0006302\",\"description\":\"double-strand break repair\",\"qValue\":2.7009293975524925E-17,\"sample\":12,\"total\":97},{\"name\":\"GO:0000724\",\"description\":\"double-strand break repair via homologous recombination\",\"qValue\":1.2256392241859756E-16,\"sample\":10,\"total\":46},{\"name\":\"GO:0000725\",\"description\":\"recombinational repair\",\"qValue\":1.2256392241859756E-16,\"sample\":10,\"total\":46},{\"name\":\"GO:0016887\",\"description\":\"ATPase activity\",\"qValue\":1.8073234395335116E-15,\"sample\":13,\"total\":196},{\"name\":\"GO:0006260\",\"description\":\"DNA replication\",\"qValue\":2.8641557109411272E-15,\"sample\":13,\"total\":204},{\"name\":\"GO:0003690\",\"description\":\"double-stranded DNA binding\",\"qValue\":6.2326068252733355E-15,\"sample\":11,\"total\":105},{\"name\":\"GO:0003697\",\"description\":\"single-stranded DNA binding\",\"qValue\":2.7593675675470102E-14,\"sample\":9,\"total\":47},{\"name\":\"GO:0042623\",\"description\":\"ATPase activity, coupled\",\"qValue\":2.7272935124120397E-13,\"sample\":11,\"total\":148},{\"name\":\"GO:0006312\",\"description\":\"mitotic recombination\",\"qValue\":2.812560077458189E-13,\"sample\":8,\"total\":34},{\"name\":\"GO:0006298\",\"description\":\"mismatch repair\",\"qValue\":3.853264875489922E-13,\"sample\":7,\"total\":18},{\"name\":\"GO:0000228\",\"description\":\"nuclear chromosome\",\"qValue\":5.70132407152189E-13,\"sample\":12,\"total\":229},{\"name\":\"GO:0000018\",\"description\":\"regulation of DNA recombination\",\"qValue\":9.680177135911131E-12,\"sample\":7,\"total\":27},{\"name\":\"GO:0006261\",\"description\":\"DNA-dependent DNA replication\",\"qValue\":1.0116643423508437E-11,\"sample\":9,\"total\":90},{\"name\":\"GO:0000723\",\"description\":\"telomere maintenance\",\"qValue\":2.2920042964379676E-11,\"sample\":8,\"total\":58},{\"name\":\"GO:0032200\",\"description\":\"telomere organization\",\"qValue\":2.542791857329261E-11,\"sample\":8,\"total\":59},{\"name\":\"GO:0010833\",\"description\":\"telomere maintenance via telomere lengthening\",\"qValue\":1.1502888027113759E-10,\"sample\":7,\"total\":38},{\"name\":\"GO:0051052\",\"description\":\"regulation of DNA metabolic process\",\"qValue\":1.1396537783925926E-9,\"sample\":9,\"total\":153},{\"name\":\"GO:0032404\",\"description\":\"mismatch repair complex binding\",\"qValue\":1.2757605075498273E-9,\"sample\":5,\"total\":10},{\"name\":\"GO:0060249\",\"description\":\"anatomical structure homeostasis\",\"qValue\":5.913718218004708E-9,\"sample\":8,\"total\":116},{\"name\":\"GO:0003678\",\"description\":\"DNA helicase activity\",\"qValue\":1.6930838078614553E-8,\"sample\":6,\"total\":38},{\"name\":\"GO:0051053\",\"description\":\"negative regulation of DNA metabolic process\",\"qValue\":9.307080640329071E-8,\"sample\":6,\"total\":50},{\"name\":\"GO:0032508\",\"description\":\"DNA duplex unwinding\",\"qValue\":1.853646624903095E-7,\"sample\":5,\"total\":24},{\"name\":\"GO:0032392\",\"description\":\"DNA geometric change\",\"qValue\":2.7756100577332525E-7,\"sample\":5,\"total\":26},{\"name\":\"GO:0016445\",\"description\":\"somatic diversification of immunoglobulins\",\"qValue\":3.302556464171889E-7,\"sample\":5,\"total\":27},{\"name\":\"GO:0044454\",\"description\":\"nuclear chromosome part\",\"qValue\":3.3125207634271384E-7,\"sample\":8,\"total\":196},{\"name\":\"GO:0004386\",\"description\":\"helicase activity\",\"qValue\":3.723322536542375E-7,\"sample\":6,\"total\":64},{\"name\":\"GO:0002200\",\"description\":\"somatic diversification of immune receptors\",\"qValue\":5.339156927811979E-7,\"sample\":5,\"total\":30},{\"name\":\"GO:0002377\",\"description\":\"immunoglobulin production\",\"qValue\":1.3661038923336387E-6,\"sample\":5,\"total\":36},{\"name\":\"GO:0000794\",\"description\":\"condensed nuclear chromosome\",\"qValue\":1.5373406084428686E-6,\"sample\":5,\"total\":37},{\"name\":\"GO:0000217\",\"description\":\"DNA secondary structure binding\",\"qValue\":1.8168381281395046E-6,\"sample\":4,\"total\":13},{\"name\":\"GO:0000781\",\"description\":\"chromosome, telomeric region\",\"qValue\":2.200113134302796E-6,\"sample\":5,\"total\":40},{\"name\":\"GO:0007004\",\"description\":\"telomere maintenance via telomerase\",\"qValue\":3.2193565338406233E-6,\"sample\":4,\"total\":15},{\"name\":\"GO:0000795\",\"description\":\"synaptonemal complex\",\"qValue\":3.2193565338406233E-6,\"sample\":4,\"total\":15},{\"name\":\"GO:0006278\",\"description\":\"RNA-dependent DNA replication\",\"qValue\":4.1902597202752475E-6,\"sample\":4,\"total\":16},{\"name\":\"GO:0032201\",\"description\":\"telomere maintenance via semi-conservative replication\",\"qValue\":2.3709281661856703E-5,\"sample\":4,\"total\":24},{\"name\":\"GO:0002440\",\"description\":\"production of molecular mediator of immune response\",\"qValue\":2.393881328806352E-5,\"sample\":5,\"total\":65},{\"name\":\"GO:0006200\",\"description\":\"ATP catabolic process\",\"qValue\":2.6763774408586137E-5,\"sample\":5,\"total\":67},{\"name\":\"GO:0004003\",\"description\":\"ATP-dependent DNA helicase activity\",\"qValue\":2.6763774408586137E-5,\"sample\":4,\"total\":25},{\"name\":\"GO:0000722\",\"description\":\"telomere maintenance via recombination\",\"qValue\":3.056616449754865E-5,\"sample\":4,\"total\":26},{\"name\":\"GO:0003684\",\"description\":\"damaged DNA binding\",\"qValue\":4.093402798321087E-5,\"sample\":4,\"total\":28},{\"name\":\"GO:0051329\",\"description\":\"interphase of mitotic cell cycle\",\"qValue\":5.090225225649074E-5,\"sample\":7,\"total\":258},{\"name\":\"GO:0051325\",\"description\":\"interphase\",\"qValue\":5.688217965249776E-5,\"sample\":7,\"total\":263},{\"name\":\"GO:0000793\",\"description\":\"condensed chromosome\",\"qValue\":6.734447394772544E-5,\"sample\":5,\"total\":82},{\"name\":\"GO:0006271\",\"description\":\"DNA strand elongation involved in DNA replication\",\"qValue\":8.372698396238842E-5,\"sample\":4,\"total\":34},{\"name\":\"GO:0046034\",\"description\":\"ATP metabolic process\",\"qValue\":8.372698396238842E-5,\"sample\":5,\"total\":86},{\"name\":\"GO:0022616\",\"description\":\"DNA strand elongation\",\"qValue\":1.1671829354628667E-4,\"sample\":4,\"total\":37},{\"name\":\"GO:0031954\",\"description\":\"positive regulation of protein 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checkpoint\",\"qValue\":0.012809640262329738,\"sample\":4,\"total\":132},{\"name\":\"GO:0007129\",\"description\":\"synapsis\",\"qValue\":0.025114510123394784,\"sample\":2,\"total\":10},{\"name\":\"GO:0010212\",\"description\":\"response to ionizing radiation\",\"qValue\":0.025372295509559533,\"sample\":3,\"total\":59},{\"name\":\"GO:0070192\",\"description\":\"chromosome organization involved in meiosis\",\"qValue\":0.029619620466778355,\"sample\":2,\"total\":11},{\"name\":\"GO:2000104\",\"description\":\"negative regulation of DNA-dependent DNA replication\",\"qValue\":0.029619620466778355,\"sample\":2,\"total\":11},{\"name\":\"GO:0045132\",\"description\":\"meiotic chromosome segregation\",\"qValue\":0.03510926897278407,\"sample\":2,\"total\":12},{\"name\":\"GO:0006301\",\"description\":\"postreplication repair\",\"qValue\":0.040540536490272054,\"sample\":2,\"total\":13},{\"name\":\"GO:0010165\",\"description\":\"response to 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response\",\"qValue\":0.09106339014997165,\"sample\":2,\"total\":20},{\"name\":\"GO:0002381\",\"description\":\"immunoglobulin production involved in immunoglobulin mediated immune response\",\"qValue\":0.09953346229028079,\"sample\":2,\"total\":21}]",
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"search_limit" : 20
},
"elements" : {
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"shared_name" : "H__sapiens__1_-Hs:5285773",
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},
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"shared_name" : "H__sapiens__1_-Hs:5329805",
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},
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"name" : "H__sapiens__1_-Hs:5292421",
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"annotations" : [ "GO:0000075", "GO:0031570", "GO:0010212", "GO:0051325", "GO:0000077", "GO:0006260", "GO:0051329", "GO:0008408", "GO:0004518", "GO:0004527", "GO:0009314" ],
"shared_name" : "H__sapiens__1_-Hs:5292421",
"Ensembl_Gene_ID" : "ENSG00000172613"
},
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},
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}, {
"data" : {
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"SUID" : 166,
"score" : 0.024791957200763937,
"annotation_name" : [ "ATPase activity", "mitotic recombination", "DNA helicase activity", "ATPase activity, coupled", "double-strand break repair via homologous recombination", "DNA recombination", "DNA geometric change", "helicase activity", "recombinational repair", "reciprocal meiotic recombination", "DNA duplex unwinding", "meiosis I", "M phase of meiotic cell cycle", "meiosis", "DNA-dependent ATPase activity", "reciprocal DNA recombination", "meiotic cell cycle", "DNA repair", "DNA conformation change", "double-strand break repair" ],
"node_type" : "result",
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"gene_name" : "RAD54B",
"name" : "H__sapiens__1_-Hs:5296680",
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