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Coexpression cluster:C1922: Difference between revisions

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|full_id=C1922_renal_mesothelioma_serous_Renal_glioblastoma_Skeletal_lung
|full_id=C1922_renal_mesothelioma_serous_Renal_glioblastoma_Skeletal_lung
|id=C1922
|id=C1922
|ontology_enrichment_celltype=CL:0000222!1.48e-28!119;CL:0000220!7.10e-17!246;CL:0002321!1.13e-16!248;CL:0000213!3.73e-16!57;CL:0000215!3.73e-16!57;CL:0002139!7.94e-15!24;CL:0000055!1.59e-14!180;CL:0002078!2.85e-14!44;CL:0000115!1.59e-12!35;CL:0000183!2.81e-12!59;CL:1000497!1.42e-11!18;CL:0002518!1.42e-11!18;CL:0000071!1.89e-11!18;CL:0002546!1.89e-11!18;CL:0000680!2.51e-11!57;CL:0000056!2.51e-11!57;CL:0000355!2.51e-11!57;CL:0000393!4.16e-11!60;CL:0000211!4.16e-11!60;CL:0000187!9.17e-11!54;CL:1000449!3.09e-10!16;CL:0000359!5.37e-09!32;CL:0002681!2.92e-08!13;CL:0002584!2.92e-08!13;CL:1000507!3.63e-08!12;CL:1000494!3.63e-08!12;CL:0000066!3.91e-08!254;CL:0000192!4.19e-08!42;CL:0000514!4.19e-08!42
|ontology_enrichment_celltype=CL:0002139!1.90e-22!24;CL:0000071!4.77e-18!18;CL:0002546!4.77e-18!18;CL:0002078!1.10e-16!45;CL:0000115!8.75e-16!36;CL:0000213!2.63e-15!58;CL:0000215!2.63e-15!58;CL:0000222!5.52e-15!121;CL:1000497!2.89e-13!17;CL:0002518!2.89e-13!17;CL:1000507!7.86e-12!10;CL:1000494!7.86e-12!10;CL:1000449!8.49e-11!15;CL:0002681!2.63e-09!12;CL:0002584!2.63e-09!12;CL:0002543!2.84e-09!6;CL:0002321!4.74e-09!250;CL:0000066!7.16e-09!253;CL:1000413!4.71e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!1.89e-29!118;UBERON:0000483!1.66e-22!309;UBERON:0000119!1.79e-22!312;UBERON:0002100!1.10e-21!216;UBERON:0004111!1.25e-20!241;UBERON:0004872!2.65e-20!84;UBERON:0000025!4.65e-20!194;UBERON:0002049!5.06e-20!79;UBERON:0007798!5.06e-20!79;UBERON:0000477!1.60e-19!286;UBERON:0000490!2.07e-19!138;UBERON:0005256!2.35e-19!143;UBERON:0000055!1.62e-18!69;UBERON:0001981!1.17e-17!60;UBERON:0007500!1.17e-17!60;UBERON:0004537!1.17e-17!60;UBERON:0006965!1.17e-17!60;UBERON:0000481!4.80e-15!347;UBERON:0003104!5.87e-15!238;UBERON:0009142!5.87e-15!238;UBERON:0000475!5.10e-14!365;UBERON:0001009!6.42e-14!113;UBERON:0004535!1.04e-13!110;UBERON:0001637!2.95e-13!42;UBERON:0003509!2.95e-13!42;UBERON:0004572!2.95e-13!42;UBERON:0000468!1.18e-12!659;UBERON:0000487!2.15e-12!22;UBERON:0002385!2.52e-12!63;UBERON:0001015!2.52e-12!63;UBERON:0000383!2.52e-12!63;UBERON:0000058!6.79e-12!26;UBERON:0001134!7.39e-12!61;UBERON:0002036!7.39e-12!61;UBERON:0003082!7.39e-12!61;UBERON:0006914!1.00e-11!25;UBERON:0003103!1.19e-11!69;UBERON:0001986!1.89e-11!18;UBERON:0004638!1.89e-11!18;UBERON:0004852!1.89e-11!18;UBERON:0000467!2.45e-11!625;UBERON:0004290!3.11e-11!70;UBERON:0000480!4.01e-11!626;UBERON:0000080!1.43e-10!18;UBERON:0002120!1.43e-10!18;UBERON:0004875!1.43e-10!18;UBERON:0005721!1.43e-10!18;UBERON:0005754!1.43e-10!18;UBERON:0007297!1.43e-10!18;UBERON:0004573!1.56e-10!33;UBERON:0004571!1.56e-10!33;UBERON:0006555!1.88e-10!17;UBERON:0005103!1.88e-10!17;UBERON:0000083!1.88e-10!17;UBERON:0009201!1.88e-10!17;UBERON:0004819!1.88e-10!17;UBERON:0006553!1.88e-10!17;UBERON:0003074!1.88e-10!17;UBERON:0003060!1.88e-10!17;UBERON:0000914!2.58e-10!83;UBERON:0002329!2.58e-10!83;UBERON:0003077!2.58e-10!83;UBERON:0003059!2.58e-10!83;UBERON:0007282!2.58e-10!83;UBERON:0009618!2.58e-10!83;UBERON:0007285!2.58e-10!83;UBERON:0002050!3.06e-10!605;UBERON:0005423!3.06e-10!605;UBERON:0004211!3.09e-10!16;UBERON:0001285!3.09e-10!16;UBERON:0007684!3.09e-10!16;UBERON:0003220!3.09e-10!16;UBERON:0004208!3.09e-10!16;UBERON:0003886!3.65e-10!63;UBERON:0000922!4.54e-10!612;UBERON:0000923!4.71e-10!604;UBERON:0005291!4.71e-10!604;UBERON:0006598!4.71e-10!604;UBERON:0002532!4.71e-10!604;UBERON:0000489!6.77e-10!32;UBERON:0002113!7.78e-10!27;UBERON:0003918!7.78e-10!27;UBERON:0005095!7.78e-10!27;UBERON:0007687!7.78e-10!27;UBERON:0004876!9.55e-10!20;UBERON:0000486!2.64e-09!82;UBERON:0000926!3.82e-09!448;UBERON:0004120!3.82e-09!448;UBERON:0006603!3.82e-09!448;UBERON:0001008!4.11e-09!45;UBERON:0006554!6.70e-09!44;UBERON:0003064!6.87e-09!37;UBERON:0003887!8.29e-09!21;UBERON:0009569!9.64e-09!113;UBERON:0000466!2.43e-08!126;UBERON:0001225!2.92e-08!13;UBERON:0008987!2.92e-08!13;UBERON:0009773!3.63e-08!12;UBERON:0001231!3.63e-08!12;UBERON:0004810!3.63e-08!12;UBERON:0002417!4.52e-08!61;UBERON:0000916!4.52e-08!61;UBERON:0002553!5.25e-08!70;UBERON:0000947!1.39e-07!21;UBERON:0010191!1.39e-07!21;UBERON:0005172!2.11e-07!55;UBERON:0005173!2.11e-07!55;UBERON:0000353!2.60e-07!17;UBERON:0005177!4.71e-07!107;UBERON:0001851!4.95e-07!16;UBERON:0000464!5.78e-07!104
|ontology_enrichment_uberon=UBERON:0003914!7.48e-20!117;UBERON:0004638!4.77e-18!18;UBERON:0001986!4.77e-18!18;UBERON:0004852!4.77e-18!18;UBERON:0000487!8.60e-14!22;UBERON:0000025!6.24e-13!192;UBERON:0004111!1.71e-12!240;UBERON:0000055!4.38e-12!68;UBERON:0002100!5.30e-12!199;UBERON:0004810!7.86e-12!10;UBERON:0002049!1.11e-11!78;UBERON:0007798!1.11e-11!78;UBERON:0002113!1.29e-11!26;UBERON:0003918!1.29e-11!26;UBERON:0011143!1.29e-11!26;UBERON:0005095!1.29e-11!26;UBERON:0007687!1.29e-11!26;UBERON:0006555!1.29e-11!16;UBERON:0004819!1.29e-11!16;UBERON:0006914!1.61e-11!25;UBERON:0000119!6.32e-11!309;UBERON:0004211!8.49e-11!15;UBERON:0009773!8.49e-11!15;UBERON:0001231!8.49e-11!15;UBERON:0001285!8.49e-11!15;UBERON:0007684!8.49e-11!15;UBERON:0004208!8.49e-11!15;UBERON:0000477!8.77e-11!373;UBERON:0004872!1.02e-10!83;UBERON:0004535!1.70e-10!109;UBERON:0000483!2.10e-10!306;UBERON:0001009!6.69e-10!112;UBERON:0007500!8.02e-10!59;UBERON:0001981!8.02e-10!59;UBERON:0004537!8.02e-10!59;UBERON:0006965!8.02e-10!59;UBERON:0001225!2.63e-09!12;UBERON:0008987!2.63e-09!12;UBERON:0000489!6.29e-09!31;UBERON:0000490!8.94e-09!148;UBERON:0002417!1.39e-08!60;UBERON:0000916!1.39e-08!60;UBERON:0000475!1.49e-08!264;UBERON:0001851!1.96e-08!15;UBERON:0003103!2.69e-08!68;UBERON:0009569!3.91e-08!112;UBERON:0005172!9.69e-08!54;UBERON:0005173!9.69e-08!54;UBERON:0005177!2.07e-07!101;UBERON:0003104!3.38e-07!160;UBERON:0009142!3.38e-07!160;UBERON:0003915!4.71e-07!9;UBERON:0004700!4.71e-07!9;UBERON:0001917!4.71e-07!9;UBERON:0000353!5.84e-07!15
|tf_chipseq_enrich=FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000389680317155907!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101267165130182!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.000109233669207383!NR3C1#2908;5:14.973023331173:1.32777388277837e-06:5.25469407137135e-05
|tf_chipseq_enrich=FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000389680317155907!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101267165130182!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.000109233669207383!NR3C1#2908;5:14.973023331173:1.32777388277837e-06:5.25469407137135e-05
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6467,0.0912686,0.425114,0.7034,0.218241,0.0242146,0.10708,0.327369,0.0656876,0.12998,2.92185e-07,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.510703,0.33844,0.0649137,4.23769e-06,0.0638093,0.195675,0.0162521,0.176557,0.396547,0.0472148,0.383224,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.334921,0.296227,0.208788,0.00169887,0.36304,0.430936,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.0197126,0.00309105,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.855975,0.629422,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.00239491,0.056055,0.120552,0.41771,0.893893,0.830533,0.335207,0.434016,0.190688,0.299739,0.278645,0.0454186,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.98236,0.989834,0.319826,0.0643195,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.000198588,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.0151089,0.0663381,0.0934526,0.000100497,0.123404,0.430769,0.240825,0.0515122,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.689826,0.245965,0.116923,0.0116046,0.0983658,0.0284215,0.238223,0.156976,1.15137e-05,0.267391,0.301441,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,1.72391e-06,0.273972,0.153023,0.0152397,0.0834173,0.000138311,0.160699,0.391307,0.0147448,0.181253,0.0422294,0.0383597,0.146486,0.183121,0.262486,0.294204,0.131936,0.288826,0.246621,4.19643e-06,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.800557,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.00356084,0.581874,0.355154,0.730614,0.0739871,0.537088,0.603804,0.0789735,0.306963,0.569605,0.0401862,0.580285,0.0473662,0.764863,0.820986,0.610475,0.881697,0.200159,0.672416,0.111362,0.623136,0.349408,0.96913,0.967174,0.349068,0.70429,0.798758,0.0494957,0.000284645,0.326931,0.737642,0.886619,0.111685,0.000262284,0.0212289,0.432123,0.416657,0.661773,0.494975,0.651196,0.0142241,0.626931,0.371758,0.91821,0.0513067,0.890566,0.85279,0.254547,0.901563,0.821811,0.680843,0.931136,0.0445246,0.922893,0.660884,0.922144,0.898765,0.104059,0.315485,0.311289,5.03367e-05,0.0226885,0.389888,0.603509,0.511254,0.00019131,0.246387,0.224252,0.22199,0.155054,0.466978,0.518234,3.93025e-11,0.353942,0.0197899,0.427276,0.747776,0.466967,0.283682,0.424668,0.919825,0.00598529,0.583101,0.702164,0.477016,0.000520721,0.498956,0.792095,0.00154126,0.349033,0.932831,0.723248,0.34194,0.226858,0.592314,0.27725,0.89036,0.763919,0.317485,8.51845e-05,0.220564,0.845182,0.037907,0.307462,0.135076,0.469588,0.664443,0.274593,0.147074,0.541363,0.709432,0.0589911,0.531474,0.720644,0.200667,0.528646,0.361524,0.31558,0.000229189,0.00130286,0.62698,0.513592,0.0173299,0.815658,0.45585,0.36864,0.538745,0.456862,0.453004,0.680686,0.557093,0.693441,0.382214,0.553161,0.639572,2.73061e-12,0.000885649,0.694478,0.306231,0.00569755,5.10702e-13,0.784543,0.457741,1.38664e-06,0.426239,0.162155,0.656093,0.572661,0.412586,0.534679,0.41502,2.22684e-06,0.66153,0.523749,0.499347,0.307426,0.790204,0.00970047,0.000665742,0.714189,0.44799,0.813041,0.318338,0.276338,0.126433,0.102654,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.0854897,0.54721,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.343265,0.501812,0.0251441,0.336254,0.053444,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.00470669,0.348739,0.419895,0.138495,0.208834,0.32256,0.082459,0.00899032,0.109684,0.322704,0.00019998,0.181288,0.0289693,0.352328,0.255358,0.351665,0.265112,0.00204916,0.00602216,0.0854747,0.0747609,8.56475e-08,0.312881,0.162482,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.0655592,0.303699,0.198326,0.394084,0.458518,0.282501,0.00328682,0.390891,0.00274742,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.0148293,0.316002,0.0618069,0.321404,0.225079,0.050521,0.379651,0.185715,8.02553e-05,0.375521,0.271405,0.0544127,0.221943,4.03451e-05,0.0114324,0.00021503,0.208775,0.390438,0.00904736,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.00276944,0.126615,0.0669467,0.0879453,0.474066,0.0919467,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.00020432,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.000186738,0.00166177,0.000594394,6.09666e-06,0.11881,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,5.82624e-06,0.185476,0.336314,7.88714e-05,0.184651,0.303359,0.297596,0.42392,0.00254622,0.380826,0.259046,0.345068,0.151046,0.142558,0.347171,0.321735,0.15463,0.13907,4.75608e-06,0.269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}}
}}

Revision as of 11:51, 19 October 2012


Full id: C1922_renal_mesothelioma_serous_Renal_glioblastoma_Skeletal_lung



Phase1 CAGE Peaks

Hg19::chr3:149260161..149260281,-p2@WWTR1
Hg19::chr3:149260294..149260308,-p12@WWTR1
Hg19::chr3:149260318..149260331,-p14@WWTR1
Hg19::chr3:149260344..149260358,-p18@WWTR1
Hg19::chr3:149260370..149260390,-p21@WWTR1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
epithelial tube7.48e-20117
blood vessel endothelium4.77e-1818
endothelium4.77e-1818
cardiovascular system endothelium4.77e-1818
simple squamous epithelium8.60e-1422
tube6.24e-13192
anatomical conduit1.71e-12240
vessel4.38e-1268
trunk5.30e-12199
nephron tubule epithelium7.86e-1210
vasculature1.11e-1178
vascular system1.11e-1178
kidney1.29e-1126
kidney mesenchyme1.29e-1126
upper urinary tract1.29e-1126
kidney rudiment1.29e-1126
kidney field1.29e-1126
excretory tube1.29e-1116
kidney epithelium1.29e-1116
squamous epithelium1.61e-1125
cell layer6.32e-11309
nephron epithelium8.49e-1115
renal tubule8.49e-1115
nephron tubule8.49e-1115
nephron8.49e-1115
uriniferous tubule8.49e-1115
nephrogenic mesenchyme8.49e-1115
anatomical cluster8.77e-11373
splanchnic layer of lateral plate mesoderm1.02e-1083
cardiovascular system1.70e-10109
epithelium2.10e-10306
circulatory system6.69e-10112
epithelial tube open at both ends8.02e-1059
blood vessel8.02e-1059
blood vasculature8.02e-1059
vascular cord8.02e-1059
cortex of kidney2.63e-0912
renal parenchyma2.63e-0912
cavitated compound organ6.29e-0931
unilaminar epithelium8.94e-09148
abdominal segment of trunk1.39e-0860
abdomen1.39e-0860
organism subdivision1.49e-08264
cortex1.96e-0815
compound organ2.69e-0868
subdivision of trunk3.91e-08112
abdomen element9.69e-0854
abdominal segment element9.69e-0854
trunk region element2.07e-07101
mesenchyme3.38e-07160
entire embryonic mesenchyme3.38e-07160
endothelial tube4.71e-079
arterial system endothelium4.71e-079
endothelium of artery4.71e-079
parenchyma5.84e-0715


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235358.99795530889441.69470025615156e-050.000389680317155907
GATA2#2624512.7449317335542.9719152914525e-060.000101267165130182
JUN#3725512.51282919233633.25800591331781e-060.000109233669207383
NR3C1#2908514.9730233311731.32777388277837e-065.25469407137135e-05



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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