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Coexpression cluster:C860: Difference between revisions

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|ontology_enrichment_disease=DOID:299!8.44e-14!25;DOID:193!4.81e-12!29;DOID:120!8.69e-11!27;DOID:305!9.57e-09!106;DOID:0050687!1.62e-08!143
|ontology_enrichment_disease=DOID:299!8.44e-14!25;DOID:193!4.81e-12!29;DOID:120!8.69e-11!27;DOID:305!9.57e-09!106;DOID:0050687!1.62e-08!143
|ontology_enrichment_uberon=UBERON:0000466!3.48e-14!126;UBERON:0005172!5.11e-14!55;UBERON:0005173!5.11e-14!55;UBERON:0000481!8.17e-14!347;UBERON:0002346!1.09e-13!90;UBERON:0002113!2.04e-13!27;UBERON:0003918!2.04e-13!27;UBERON:0005095!2.04e-13!27;UBERON:0007687!2.04e-13!27;UBERON:0000062!4.34e-13!511;UBERON:0000489!5.27e-13!32;UBERON:0003075!1.60e-12!86;UBERON:0007284!1.60e-12!86;UBERON:0006554!3.46e-12!44;UBERON:0002553!4.28e-12!70;UBERON:0003064!5.57e-12!37;UBERON:0003929!8.86e-12!54;UBERON:0001008!1.12e-11!45;UBERON:0003886!1.53e-11!63;UBERON:0005177!1.81e-11!107;UBERON:0000080!2.18e-11!18;UBERON:0002120!2.18e-11!18;UBERON:0004875!2.18e-11!18;UBERON:0005721!2.18e-11!18;UBERON:0005754!2.18e-11!18;UBERON:0007297!2.18e-11!18;UBERON:0002417!2.26e-11!61;UBERON:0000916!2.26e-11!61;UBERON:0000464!2.50e-11!104;UBERON:0007023!2.70e-11!115;UBERON:0005156!2.87e-11!59;UBERON:0000990!2.87e-11!59;UBERON:0004876!7.52e-11!20;UBERON:0006555!9.79e-11!17;UBERON:0005103!9.79e-11!17;UBERON:0000083!9.79e-11!17;UBERON:0009201!9.79e-11!17;UBERON:0004819!9.79e-11!17;UBERON:0006553!9.79e-11!17;UBERON:0003074!9.79e-11!17;UBERON:0003060!9.79e-11!17;UBERON:0005911!1.35e-10!82;UBERON:0000058!1.78e-10!26;UBERON:0004211!7.30e-10!16;UBERON:0001285!7.30e-10!16;UBERON:0007684!7.30e-10!16;UBERON:0003220!7.30e-10!16;UBERON:0004208!7.30e-10!16;UBERON:0003056!1.39e-09!61;UBERON:0000483!1.83e-09!309;UBERON:0003133!1.98e-09!48;UBERON:0000475!2.75e-09!365;UBERON:0000119!4.39e-09!312;UBERON:0003887!6.20e-09!21;UBERON:0001048!6.42e-09!168;UBERON:0009569!6.74e-09!113;UBERON:0009773!8.03e-09!12;UBERON:0001231!8.03e-09!12;UBERON:0004810!8.03e-09!12;UBERON:0007625!1.41e-08!11;UBERON:0000073!1.49e-08!94;UBERON:0001016!1.49e-08!94;UBERON:0000153!4.39e-08!129;UBERON:0007811!4.39e-08!129;UBERON:0005743!8.20e-08!86;UBERON:0001851!8.53e-08!16;UBERON:0001007!9.03e-08!155;UBERON:0001555!9.03e-08!155;UBERON:0007026!9.03e-08!155;UBERON:0001049!1.05e-07!57;UBERON:0005068!1.05e-07!57;UBERON:0006241!1.05e-07!57;UBERON:0007135!1.05e-07!57;UBERON:0000924!1.13e-07!173;UBERON:0006601!1.13e-07!173;UBERON:0000922!1.28e-07!612;UBERON:0003101!1.56e-07!22;UBERON:0000079!1.56e-07!22;UBERON:0000991!1.84e-07!21;UBERON:0009196!1.84e-07!21;UBERON:0009117!1.84e-07!21;UBERON:0005564!1.84e-07!21;UBERON:0000033!1.86e-07!123;UBERON:0000064!1.90e-07!219;UBERON:0002616!2.91e-07!59;UBERON:0001225!3.52e-07!13;UBERON:0008987!3.52e-07!13;UBERON:0002050!5.78e-07!605;UBERON:0005423!5.78e-07!605;UBERON:0004176!6.69e-07!22;UBERON:0004121!6.75e-07!169;UBERON:0004921!8.56e-07!129;UBERON:0004185!8.56e-07!129;UBERON:0000468!8.93e-07!659
|ontology_enrichment_uberon=UBERON:0000466!3.48e-14!126;UBERON:0005172!5.11e-14!55;UBERON:0005173!5.11e-14!55;UBERON:0000481!8.17e-14!347;UBERON:0002346!1.09e-13!90;UBERON:0002113!2.04e-13!27;UBERON:0003918!2.04e-13!27;UBERON:0005095!2.04e-13!27;UBERON:0007687!2.04e-13!27;UBERON:0000062!4.34e-13!511;UBERON:0000489!5.27e-13!32;UBERON:0003075!1.60e-12!86;UBERON:0007284!1.60e-12!86;UBERON:0006554!3.46e-12!44;UBERON:0002553!4.28e-12!70;UBERON:0003064!5.57e-12!37;UBERON:0003929!8.86e-12!54;UBERON:0001008!1.12e-11!45;UBERON:0003886!1.53e-11!63;UBERON:0005177!1.81e-11!107;UBERON:0000080!2.18e-11!18;UBERON:0002120!2.18e-11!18;UBERON:0004875!2.18e-11!18;UBERON:0005721!2.18e-11!18;UBERON:0005754!2.18e-11!18;UBERON:0007297!2.18e-11!18;UBERON:0002417!2.26e-11!61;UBERON:0000916!2.26e-11!61;UBERON:0000464!2.50e-11!104;UBERON:0007023!2.70e-11!115;UBERON:0005156!2.87e-11!59;UBERON:0000990!2.87e-11!59;UBERON:0004876!7.52e-11!20;UBERON:0006555!9.79e-11!17;UBERON:0005103!9.79e-11!17;UBERON:0000083!9.79e-11!17;UBERON:0009201!9.79e-11!17;UBERON:0004819!9.79e-11!17;UBERON:0006553!9.79e-11!17;UBERON:0003074!9.79e-11!17;UBERON:0003060!9.79e-11!17;UBERON:0005911!1.35e-10!82;UBERON:0000058!1.78e-10!26;UBERON:0004211!7.30e-10!16;UBERON:0001285!7.30e-10!16;UBERON:0007684!7.30e-10!16;UBERON:0003220!7.30e-10!16;UBERON:0004208!7.30e-10!16;UBERON:0003056!1.39e-09!61;UBERON:0000483!1.83e-09!309;UBERON:0003133!1.98e-09!48;UBERON:0000475!2.75e-09!365;UBERON:0000119!4.39e-09!312;UBERON:0003887!6.20e-09!21;UBERON:0001048!6.42e-09!168;UBERON:0009569!6.74e-09!113;UBERON:0009773!8.03e-09!12;UBERON:0001231!8.03e-09!12;UBERON:0004810!8.03e-09!12;UBERON:0007625!1.41e-08!11;UBERON:0000073!1.49e-08!94;UBERON:0001016!1.49e-08!94;UBERON:0000153!4.39e-08!129;UBERON:0007811!4.39e-08!129;UBERON:0005743!8.20e-08!86;UBERON:0001851!8.53e-08!16;UBERON:0001007!9.03e-08!155;UBERON:0001555!9.03e-08!155;UBERON:0007026!9.03e-08!155;UBERON:0001049!1.05e-07!57;UBERON:0005068!1.05e-07!57;UBERON:0006241!1.05e-07!57;UBERON:0007135!1.05e-07!57;UBERON:0000924!1.13e-07!173;UBERON:0006601!1.13e-07!173;UBERON:0000922!1.28e-07!612;UBERON:0003101!1.56e-07!22;UBERON:0000079!1.56e-07!22;UBERON:0000991!1.84e-07!21;UBERON:0009196!1.84e-07!21;UBERON:0009117!1.84e-07!21;UBERON:0005564!1.84e-07!21;UBERON:0000033!1.86e-07!123;UBERON:0000064!1.90e-07!219;UBERON:0002616!2.91e-07!59;UBERON:0001225!3.52e-07!13;UBERON:0008987!3.52e-07!13;UBERON:0002050!5.78e-07!605;UBERON:0005423!5.78e-07!605;UBERON:0004176!6.69e-07!22;UBERON:0004121!6.75e-07!169;UBERON:0004921!8.56e-07!129;UBERON:0004185!8.56e-07!129;UBERON:0000468!8.93e-07!659
|tf_chipseq_enrich=CEBPB#1051;6:4.78268857549489:0.000520075535673016:0.0045060700904392!CTCF#10664;6:3.21615382384502:0.00442909532615486:0.0209706359039028!GABPB1#2553;6:4.2406103017093:0.00100657891610646:0.00721177851541763!HDAC2#3066;6:8.04937214197576:2.76518202234458e-05:0.000584719265502421!MYC#4609;6:3.13336912296564:0.00507742326845552:0.0236310609952864!TCF7L2#6934;6:6.46210593788241:9.65893777244962e-05:0.00137509514996846
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02558,0.153887,0.473193,0.786122,0.106051,0.760589,0.562338,0.125614,0.185352,0.836596,0.353062,0.319022,0.321942,0.0196184,0.0922004,0.929835,0.405772,0.123725,0.000283023,0.171937,0.000203364,0.622957,0.557671,0.504704,0.373984,0.234869,0.594282,0.00109696,0.231968,0.468003,0.247799,0.48957,0.743386,0.412992,0.398555,0.456726,0.0917717,0.266963,0.709133,0.67635,0.149158,0.282725,0.859952,0.378291,0.235602,0.319841,0.367901,0.374858,0.979257,0.862672,0.162583,0.294593,0.157267,0.191637,0.230272,0.279473,0.404631,0.108968,0.22657,0.660939,0.988741,0.00365741,0.55805,0.679662,0.345014,0.509635,0.139728,0.929056,0.179342,0.150014,0.81061,0.188879,0.47404,0.696314,0.218579,0.570357,0.68237,0.113765,0.36072,0.47356,0.999689,0.998948,0.537364,0.559783,0.317505,0.20738,0.318705,0.155403,0.28528,0.535959,0.230462,0.144238,0.322438,0.215644,0.574582,0.426136,0.120206,0.377654,0.142291,0.16868,0.332605,0.277625,0.467862,0.308973,0.56623,0.178172,0.223814,0.23158,0.675976,0.423653,0.514609,0.198712,0.300338,0.732963,0.132915,0.0138538,0.421894,0.194062,0.507323,0.415,0.903792,0.431432,0.220174,0.274822,0.187056,0.405162,0.419696,0.289311,0.429656,0.463283,0.512016,0.388586,0.578187,0.619193,0.67784,0.344554,0.253271,0.738717,0.329845,0.328599,0.151851,0.472883,0.28263,0.640164,0.615079,0.396379,0.295573,0.629492,0.305672,0.329653,0.0826755,0.458123,0.271514,0.562239,0.456073,0.501852,0.246465,0.494232,0.43242,0.712293,0.908417,0.183756,0.612124,0.480538,0.559853,0.583498,0.825084,0.960223,0.115301,0.829864,0.080776,0.137664,0.380034,0.835545,0.784815,0.590452,0.825171,0.584173,0.927431,0.854868,0.0205438,0.843029,0.000225263,0.5197,0.81476,0.0650396,0.517961,0.797945,0.944711,0.857696,0.84827,0.140542,0.807884,0.892689,0.90117,0.857974,0.915143,0.999047,0.998922,0.576288,0.912555,0.959502,0.22404,0.102928,0.678796,0.931168,0.43998,0.679307,0.45002,0.0592463,0.677516,0.942119,0.885602,0.74495,0.878336,0.630525,0.137857,0.238387,0.99331,0.808521,0.988024,0.978329,0.444299,0.99031,0.968249,0.898139,0.995258,0.789666,0.994054,0.885,0.993938,0.989751,0.992758,0.53144,0.525677,0.535663,0.696179,0.25991,0.282856,0.761127,0.478676,0.432068,0.398215,0.829626,0.286066,0.358365,0.0607944,0.120718,0.582609,0.347515,0.671987,0.936383,0.715876,0.486888,0.0261585,0.961129,0.827981,0.522068,0.911294,0.726487,0.870127,0.748955,0.820992,0.804619,0.447102,0.995488,0.257328,0.566957,0.108129,0.26791,0.612802,0.987979,0.944266,0.534174,0.59603,0.39248,0.976031,0.455938,0.520391,0.251906,0.718663,0.641495,0.473785,0.390604,0.789652,0.91557,0.826633,0.780483,0.92196,0.808423,0.777825,0.592348,0.53157,0.655131,0.0221116,0.315811,2.89967e-06,0.658205,0.127183,0.0352678,0.601385,0.787244,0.125051,0.700795,0.197238,0.00656391,0.906021,0.618341,0.800335,0.0564212,0.678726,0.563598,0.906657,0.166731,0.507693,0.614484,0.953578,0.346038,0.15243,0.670798,0.936954,0.881728,0.506865,0.092452,0.783476,0.657798,0.480941,0.885438,0.773185,0.402521,0.520341,0.955985,0.485241,0.048116,0.918312,0.695285,0.247257,0.0427197,0.476313,0.236882,0.293843,0.535113,0.108025,0.156154,0.631577,0.501058,0.220257,0.641475,0.119072,0.158132,0.11971,0.562098,0.183097,0.269945,0.284002,0.454236,0.620409,0.794982,0.626018,0.53945,0.587396,0.141724,0.51191,0.564853,0.568699,0.751808,0.351828,0.559441,0.521951,0.498061,0.355143,0.523646,0.10457,0.278571,0.35692,0.483693,0.575859,0.0249439,0.257808,0.374056,0.541075,0.612576,0.567518,0.207337,0.54127,0.0865259,0.00792884,0.408394,0.580521,0.445508,0.579662,0.459939,0.122652,0.203837,0.163644,0.143933,0.647708,0.527867,0.762661,0.429455,0.347441,0.292694,0.317977,0.185106,0.555523,0.437378,0.563762,0.515166,0.357319,0.632866,0.706798,0.485196,0.440503,0.628986,0.41993,0.557752,0.356596,0.492927,0.495033,0.221402,0.630984,0.636345,0.532147,0.551524,0.539507,0.399497,0.510758,0.247672,0.33694,0.208477,0.610026,0.469149,0.525556,0.394627,0.518957,0.600238,0.432878,0.373963,0.628435,0.568369,0.467238,0.477159,0.288135,0.52892,0.710278,0.666923,0.559725,0.248778,0.528779,0.313572,0.167775,0.168268,0.420832,0.237199,0.129411,0.168156,0.723393,0.636312,0.546774,0.153403,0.588091,0.503708,0.246187,0.291231,0.198269,0.351675,0.197483,0.308086,0.20448,0.232324,0.368317,0.319783,0.139615,0.206257,0.268704,0.117319,0.383259,0.0421382,0.689269,0.675716,0.758473,0.0930837,0.638663,0.626754,0.52491,0.576995,0.693079,0.622646,0.479007,0.671084,0.640709,0.375599,0.44222,0.536945,0.523194,0.676017,0.593153,0.730416,0.336551,0.559521,0.570279,0.335207,0.514691,0.506629,0.668131,0.670422,0.249066,0.450988,0.571064,0.279276,0.381344,0.210329,0.539957,0.285349,0.2588,0.362588,0.46627,0.438198,0.65176,0.217989,0.650689,0.298817,0.567905,0.475347,0.434688,0.555097,0.621443,0.536392,0.440535
}}
}}

Revision as of 12:05, 5 September 2012


Full id: C860_serous_mesothelioma_Renal_clear_colon_endometrial_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr6:24178711..24178718,-p@chr6:24178711..24178718
-
Hg19::chr6:24178792..24178829,+p@chr6:24178792..24178829
+
Hg19::chr6:24278432..24278446,-p@chr6:24278432..24278446
-
Hg19::chr6:24345366..24345371,-p@chr6:24345366..24345371
-
Hg19::chr6:24358088..24358099,-p5@DCDC2
Hg19::chr6:24358114..24358125,-p4@DCDC2
Hg19::chr6:24358146..24358176,-p1@DCDC2
Hg19::chr6:24358196..24358199,-p8@DCDC2
Hg19::chr6:24358226..24358239,-p3@DCDC2
Hg19::chr6:24358264..24358295,-p2@DCDC2


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>disease_data<br>

Cell Type
Ontology termp-valuen
kidney cell1.93e-1118
kidney epithelial cell1.93e-1118
epithelial cell of nephron7.30e-1016
kidney tubule cell8.03e-0912
nephron tubule epithelial cell8.03e-0912
epithelial cell5.12e-08254
kidney cortical cell3.52e-0713
renal cortical epithelial cell3.52e-0713
Uber Anatomy
Ontology termp-valuen
immaterial anatomical entity3.48e-14126
abdomen element5.11e-1455
abdominal segment element5.11e-1455
multi-tissue structure8.17e-14347
neurectoderm1.09e-1390
kidney2.04e-1327
kidney mesenchyme2.04e-1327
kidney rudiment2.04e-1327
kidney field2.04e-1327
organ4.34e-13511
cavitated compound organ5.27e-1332
neural plate1.60e-1286
presumptive neural plate1.60e-1286
urinary system structure3.46e-1244
anatomical cavity4.28e-1270
intermediate mesoderm5.57e-1237
gut epithelium8.86e-1254
renal system1.12e-1145
body cavity precursor1.53e-1163
trunk region element1.81e-11107
mesonephros2.18e-1118
pronephros2.18e-1118
nephrogenic cord2.18e-1118
pronephric mesoderm2.18e-1118
rostral part of nephrogenic cord2.18e-1118
presumptive pronephric mesoderm2.18e-1118
abdominal segment of trunk2.26e-1161
abdomen2.26e-1161
anatomical space2.50e-11104
adult organism2.70e-11115
reproductive structure2.87e-1159
reproductive system2.87e-1159
urogenital ridge7.52e-1120
excretory tube9.79e-1117
mesonephric epithelium9.79e-1117
mesonephric tubule9.79e-1117
nephric duct9.79e-1117
kidney epithelium9.79e-1117
renal duct9.79e-1117
mesonephric duct9.79e-1117
pronephric duct9.79e-1117
endo-epithelium1.35e-1082
duct1.78e-1026
nephron epithelium7.30e-1016
nephron7.30e-1016
uriniferous tubule7.30e-1016
metanephric mesenchyme7.30e-1016
nephrogenic mesenchyme7.30e-1016
pre-chordal neural plate1.39e-0961
epithelium1.83e-09309
reproductive organ1.98e-0948
organism subdivision2.75e-09365
cell layer4.39e-09312
intraembryonic coelom6.20e-0921
primordium6.42e-09168
subdivision of trunk6.74e-09113
renal tubule8.03e-0912
nephron tubule8.03e-0912
nephron tubule epithelium8.03e-0912
pigment epithelium of eye1.41e-0811
regional part of nervous system1.49e-0894
nervous system1.49e-0894
anterior region of body4.39e-08129
craniocervical region4.39e-08129
cortex8.53e-0816
digestive system9.03e-08155
digestive tract9.03e-08155
primitive gut9.03e-08155
neural tube1.05e-0757
neural rod1.05e-0757
future spinal cord1.05e-0757
neural keel1.05e-0757
ectoderm1.13e-07173
presumptive ectoderm1.13e-07173
embryo1.28e-07612
male organism1.56e-0722
male reproductive system1.56e-0722
gonad1.84e-0721
indifferent external genitalia1.84e-0721
indifferent gonad1.84e-0721
gonad primordium1.84e-0721
head1.86e-07123
organ part1.90e-07219
regional part of brain2.91e-0759
cortex of kidney3.52e-0713
renal parenchyma3.52e-0713
embryonic structure5.78e-07605
developing anatomical structure5.78e-07605
external genitalia6.69e-0722
ectoderm-derived structure6.75e-07169
subdivision of digestive tract8.56e-07129

Disease
Ontology termp-valuen


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)

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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
CEBPB#105164.782688575494890.0005200755356730160.0045060700904392
CTCF#1066463.216153823845020.004429095326154860.0209706359039028
GABPB1#255364.24061030170930.001006578916106460.00721177851541763
HDAC2#306668.049372141975762.76518202234458e-050.000584719265502421
MYC#460963.133369122965640.005077423268455520.0236310609952864
TCF7L2#693466.462105937882419.65893777244962e-050.00137509514996846



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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