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Coexpression cluster:C860: Difference between revisions

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|full_id=C860_serous_mesothelioma_Renal_clear_colon_endometrial_hepatoblastoma
|full_id=C860_serous_mesothelioma_Renal_clear_colon_endometrial_hepatoblastoma
|id=C860
|id=C860
|ontology_enrichment_celltype=CL:1000497!1.93e-11!18;CL:0002518!1.93e-11!18;CL:1000449!7.30e-10!16;CL:1000507!8.03e-09!12;CL:1000494!8.03e-09!12;CL:0000066!5.12e-08!254;CL:0002681!3.52e-07!13;CL:0002584!3.52e-07!13
|ontology_enrichment_celltype=CL:1000507!2.61e-22!10;CL:1000494!2.61e-22!10;CL:1000497!3.64e-20!17;CL:0002518!3.64e-20!17;CL:1000449!6.60e-17!15;CL:0002681!2.36e-11!12;CL:0002584!2.36e-11!12;CL:0000066!6.34e-11!253;CL:0000239!7.04e-08!3;CL:1000615!7.04e-08!3;CL:0002306!7.04e-08!3
|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!9.39e-15!25;DOID:193!1.01e-11!29;DOID:120!5.78e-11!27;DOID:0050687!8.42e-11!143;DOID:305!1.88e-10!106;DOID:162!2.15e-08!235;DOID:14566!5.52e-08!239;DOID:7!7.74e-08!39
|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:0005172!1.14e-24!54;UBERON:0005173!1.14e-24!54;UBERON:0002113!8.88e-24!26;UBERON:0003918!8.88e-24!26;UBERON:0011143!8.88e-24!26;UBERON:0005095!8.88e-24!26;UBERON:0007687!8.88e-24!26;UBERON:0004810!2.61e-22!10;UBERON:0002417!2.35e-21!60;UBERON:0000916!2.35e-21!60;UBERON:0000489!4.45e-19!31;UBERON:0006555!7.67e-19!16;UBERON:0004819!7.67e-19!16;UBERON:0005177!8.34e-18!101;UBERON:0009569!1.76e-17!112;UBERON:0004211!6.60e-17!15;UBERON:0009773!6.60e-17!15;UBERON:0001231!6.60e-17!15;UBERON:0001285!6.60e-17!15;UBERON:0007684!6.60e-17!15;UBERON:0004208!6.60e-17!15;UBERON:0006554!1.13e-13!47;UBERON:0001008!2.84e-13!48;UBERON:0001225!2.36e-11!12;UBERON:0008987!2.36e-11!12;UBERON:0001851!4.77e-11!15;UBERON:0000353!9.60e-09!15;UBERON:0006853!7.04e-08!3;UBERON:0007685!7.04e-08!3;UBERON:0004134!7.04e-08!3;UBERON:0003103!1.01e-07!68;UBERON:0005911!1.28e-07!82;UBERON:0002368!1.55e-07!35;UBERON:0000466!2.06e-07!117;UBERON:0003929!2.74e-07!54;UBERON:0002100!2.94e-07!199;UBERON:0002046!4.36e-07!5;UBERON:0004117!4.36e-07!5;UBERON:0007689!4.36e-07!5;UBERON:0007123!4.36e-07!5;UBERON:0003091!4.36e-07!5
|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
|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 16:48, 19 October 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>

Uber Anatomy
Ontology termp-valuen
abdomen element1.14e-2454
abdominal segment element1.14e-2454
kidney8.88e-2426
kidney mesenchyme8.88e-2426
upper urinary tract8.88e-2426
kidney rudiment8.88e-2426
kidney field8.88e-2426
nephron tubule epithelium2.61e-2210
abdominal segment of trunk2.35e-2160
abdomen2.35e-2160
cavitated compound organ4.45e-1931
excretory tube7.67e-1916
kidney epithelium7.67e-1916
trunk region element8.34e-18101
subdivision of trunk1.76e-17112
nephron epithelium6.60e-1715
renal tubule6.60e-1715
nephron tubule6.60e-1715
nephron6.60e-1715
uriniferous tubule6.60e-1715
nephrogenic mesenchyme6.60e-1715
urinary system structure1.13e-1347
renal system2.84e-1348
cortex of kidney2.36e-1112
renal parenchyma2.36e-1112
cortex4.77e-1115
parenchyma9.60e-0915
renal cortex tubule7.04e-083
region of nephron tubule7.04e-083
proximal tubule7.04e-083
compound organ1.01e-0768
endo-epithelium1.28e-0782
endocrine gland1.55e-0735
immaterial anatomical entity2.06e-07117
gut epithelium2.74e-0754
trunk2.94e-07199
thyroid gland4.36e-075
pharyngeal pouch4.36e-075
thyroid diverticulum4.36e-075
pharyngeal pouch 24.36e-075
thyroid primordium4.36e-075
Disease
Ontology termp-valuen
adenocarcinoma9.39e-1525
reproductive organ cancer1.01e-1129
female reproductive organ cancer5.78e-1127
cell type cancer8.42e-11143
carcinoma1.88e-10106
cancer2.15e-08235
disease of cellular proliferation5.52e-08239
disease of anatomical entity7.74e-0839


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
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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