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Coexpression cluster:C2387: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.06e-14!106;DOID:0050687!1.28e-10!143;DOID:299!2.94e-10!25
|ontology_enrichment_disease=DOID:305!3.06e-14!106;DOID:0050687!1.28e-10!143;DOID:299!2.94e-10!25
|ontology_enrichment_uberon=UBERON:0005177!6.30e-12!107;UBERON:0005172!4.09e-11!55;UBERON:0005173!4.09e-11!55;UBERON:0000466!1.81e-10!126;UBERON:0009569!6.67e-10!113;UBERON:0002417!6.95e-10!61;UBERON:0000916!6.95e-10!61;UBERON:0000058!2.48e-09!26;UBERON:0002113!2.73e-09!27;UBERON:0003918!2.73e-09!27;UBERON:0005095!2.73e-09!27;UBERON:0007687!2.73e-09!27;UBERON:0000489!3.57e-09!32;UBERON:0004921!2.90e-08!129;UBERON:0004185!2.90e-08!129;UBERON:0009773!5.77e-08!12;UBERON:0001231!5.77e-08!12;UBERON:0004810!5.77e-08!12;UBERON:0001008!1.86e-07!45;UBERON:0001007!3.34e-07!155;UBERON:0001555!3.34e-07!155;UBERON:0007026!3.34e-07!155;UBERON:0007499!3.84e-07!25;UBERON:0000464!4.04e-07!104;UBERON:0000481!5.68e-07!347;UBERON:0000080!6.17e-07!18;UBERON:0002120!6.17e-07!18;UBERON:0004875!6.17e-07!18;UBERON:0005721!6.17e-07!18;UBERON:0005754!6.17e-07!18;UBERON:0007297!6.17e-07!18;UBERON:0006554!6.83e-07!44
|ontology_enrichment_uberon=UBERON:0005177!6.30e-12!107;UBERON:0005172!4.09e-11!55;UBERON:0005173!4.09e-11!55;UBERON:0000466!1.81e-10!126;UBERON:0009569!6.67e-10!113;UBERON:0002417!6.95e-10!61;UBERON:0000916!6.95e-10!61;UBERON:0000058!2.48e-09!26;UBERON:0002113!2.73e-09!27;UBERON:0003918!2.73e-09!27;UBERON:0005095!2.73e-09!27;UBERON:0007687!2.73e-09!27;UBERON:0000489!3.57e-09!32;UBERON:0004921!2.90e-08!129;UBERON:0004185!2.90e-08!129;UBERON:0009773!5.77e-08!12;UBERON:0001231!5.77e-08!12;UBERON:0004810!5.77e-08!12;UBERON:0001008!1.86e-07!45;UBERON:0001007!3.34e-07!155;UBERON:0001555!3.34e-07!155;UBERON:0007026!3.34e-07!155;UBERON:0007499!3.84e-07!25;UBERON:0000464!4.04e-07!104;UBERON:0000481!5.68e-07!347;UBERON:0000080!6.17e-07!18;UBERON:0002120!6.17e-07!18;UBERON:0004875!6.17e-07!18;UBERON:0005721!6.17e-07!18;UBERON:0005754!6.17e-07!18;UBERON:0007297!6.17e-07!18;UBERON:0006554!6.83e-07!44
|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296196428790303!CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.0095394493259167!ESR1#2099;2:15.3843016480772:0.00606557262969351:0.0268367862686956!HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390666682055647!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284846527842871
|tfbs_overrepresentation=0.191353,0.00307981,0.238232,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.0143109,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.460009,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.00322261,0.113084,0.0252868,0.470097,0.00410253,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.268505,0.355976,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.327332,0.199405,0.0077267,0.347653,0.0759036,0.00969427,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.00287136,0.0174545,0.110194,0.215858,0.275495,0.182323,0.112709,0.00942364,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.701894,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.000261183,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.0476129,0.0683304,0.0447121,0.0473319,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.0146311,0.0534404,0.392741,0.0293007,0.179282,0.564569,0.0715212,0.105131,0.118265,0.182591,0.0300065,0.230552,0.0472274,0.0228403,0.159869,0.0363736,0.15105,0.0970713,0.0127261,0.0304129,0.0532055,0.108938,0.0273166,0.140245,0.241581,0.160458,0.0477937,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.00328703,0.177664,0.329956,0.346995,0.197158,0.265132,0.230439,0.00187964,0.136664,0.158184,0.147626,0.0901258,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.0234783,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.675167,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,0.15291,0.206234,0.238926,0.0313311,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.687863,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.0125608,0.0993998,0.352707,0.0834863,0.324356,0.00867491,0.113754,0.0504034,0.0152877,0.327364,0.0880794,0.869559,0.389734,0.668426,0.0854389,0.644298,0.104083,0.0114582,0.332539,0.545329,0.464128,0.389374,0.22808,0.414547,0.00499259,0.413223,0.271656,0.0406667,0.34505,0.369161,0.153719,0.00507494,0.00127744,0.702495,0.0318478,0.45167,0.234628,0.168228,0.143893,0.41477,0.279946,0.0395226,0.0262654,0.051755,0.164225,0.0806606,0.257158,0.127765,0.511459,0.0601683,0.0588752,0.350886,0.0128438,0.218919,0.398372,0.286293,0.0683688,0.127626,0.359128,0.395864,0.683133,0.368633,0.0013547,0.109035,0.0364944,0.369971,0.578349,0.537928,0.129952,0.0295245,0.714007,0.00264023,0.804772,0.402752,0.114723,0.349116,0.302142,0.239545,0.432689,0.272581,0.343881,0.377117,0.239383,0.617741,0.00342662,0.316925,0.356561,0.210197,0.0241359,0.0883859,0.0962508,0.238465,0.70198,0.853221,0.112487,0.508325,0.436735,0.0907578,0.28972,0.188468,0.280307,0.090261,0.212518,0.0596868,0.0984075,0.293026,0.0537754,0.117621,0.605423,0.0799295,0.429205,0.578951,0.365653,0.0988815,0.453022,0.35234,0.376421,0.0400268,0.0474911,0.104649,0.25441,0.202782,0.0270471,0.166182,0.00211663,0.517001,0.252778,0.483999,0.419676,0.188259,0.189182,0.477589,0.46699,0.546448,0.198922,0.058245,0.198207,0.0616078,0.178485,0.0615778,0.175552,0.129238,0.651295,0.370995,0.360161,0.429696,0.386216,0.385297,0.346931,0.0683036,0.0181818,0.360203,0.0631823,0.447838,0.289666,0.500627,0.000887405,0.122807,0.565545,0.287542,0.0387162,0.0791459,0.410093,0.179179,0.341771,0.424526,0.290547,0.0727712,0.184395,0.194887,0.0177864,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.629381,0.376317,0.433821,0.276604,0.436806,0.21267,0.00550983,0.396083,0.149061,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.00372182,0.541583,0.540322,0.247151,0.011279,0.365815,0.0576261,0.382413,0.164977,0.175633,0.139918,0.34669,0.00352963,0.4729,0.0238089,0.383126,0.0719157,0.48311,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.00171869,0.00518407,0.161297,0.168389,0.270152,0.0340965,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.00351594,0.153907,0.166608,0.227224,0.00273651,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.00571021,0.127738,0.0232207,0.161213,0.118999,0.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0737069,0.357807,0.254051,0.178782,0.019419,0.000115846,0.0408454,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.00545181,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.000708107,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.0178622,0.116818,0.389792,0.0757944,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.0705088,0.535567,0.415079,0.278645,0.365775,0.155708,0.248017,0.00244747,0.091341,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.0114526,0.0471607,0.163865,0.226359,0.960445,0.974549,0.265324,0.279778,0.141699,0.0887743,0.0106427,0.0653269,0.125712,0.264432,0.0051212,0.0604041,0.144185,0.0925862,0.0466818,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.0448074,0.0754883,0.299492,0.100006,0.362866,0.197817,0.0032479,0.279874,0.133127,0.0988568,0.223717,0.426452,0.196838,0.0826805,0.246601,7.42872e-05,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.0578865,0.0763252,0.0127656,0.110256,0.415419,0.14794,0.147307,0.00283685,0.225961,0.124417,0.0639386,0.317428,0.182843,0.00894967,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.238657,0.20272,0.0896967,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.00888122,0.154964,0.296013,0.282366,0.537932,0.459994,0.523209,0.189126,0.25423,0.146971,0.45013,0.00559995,0.472542,0.322168,0.0510811,0.174869,0.244786,0.483077,0.590496,0.603763,0.541914,0.627201,0.765905,0.934991,0.290703,0.622694,0.138899,0.478691,0.360199,0.608176,0.657141,0.519564,0.365494,0.212703,0.00164034,0.364079,0.107716,0.579886,0.421038,0.569409,0.328518,0.187186,0.310552,0.594773,0.0295909,0.528161,0.784052,0.209437,0.55323,0.401218,0.232518,0.630688,0.464001,0.60737,0.0572388,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.326516,0.16985,0.113006,0.136753,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.025886,0.39549,0.234254,0.357409,0.86719,0.365184,0.000785185,0.0171443,0.404625,0.172147,0.424691,0.715362,0.0286876,0.259048,0.635682,0.274432,0.284496,0.512545,0.162017,0.563206,0.527709,0.321001,0.263302,0.00919591,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.0585759,0.226491,0.0175854,0.0038466,0.627953,0.503881,0.454761,0.0202528,0.142363,0.452129,0.301581,0.261657,0.346776,0.131322,0.0458396,0.114247,0.349112,0.391754,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.24434,0.319747,0.475047,0.557967,0.0690544,0.282281,0.245336,0.2536,0.246827,0.564333,0.70712,0.0136122,0.00157847,0.358813,0.668972,0.574252,0.493455,0.00937114,0.125876,0.348802,0.00438353,0.579645,0.447581,0.42505,0.254628,0.713293,0.0286377,0.416962,0.264955,0.378333,0.738545,0.00382285,0.22798,0.102495,0.0703938,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.0239343,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.187728,0.231754,0.249415,0.0445044,0.0453548,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.0293669,0.290415,0.0713545,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.000605968,0.189388,0.0480552,0.000106889,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.113839,0.201057,0.15696,0.129351,0.141936,0.0786166,0.042497,0.205513,0.0442657,0.251421,0.162089,0.330223,0.387837,0.233244,0.0231432,0.327401,0.0205476,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.0567862,0.15156,0.287598,0.000621734,0.0271466,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.037179,0.390754,0.355805,0.00461365,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,1.65313e-05,0.332746,0.271338,0.242121,0.00571761,0.0326468,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.00393964,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.0164443,0.00376397,0.373453,0.0755696,0.111581,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.0588457,0.229571,0.359036,0.000845912,0.171704,0.208256,0.265058,0.256405,0.362898,0.000524161,0.0976762,0.0120812,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.0737175,0.318525,0.213257,0.0458843,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.0675312,0.0936726,0.343425,0.132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}}
}}

Revision as of 12:45, 5 September 2012


Full id: C2387_kidney_renal_serous_smallcell_clear_mesothelioma_HES3GFP



Phase1 CAGE Peaks

Hg19::chr16:71879001..71879011,+p@chr16:71879001..71879011
+
Hg19::chr1:18807489..18807496,+p3@KLHDC7A
Hg19::chr1:18807498..18807518,+p1@KLHDC7A
Hg19::chr8:107593246..107593259,+p14@OXR1


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


GO IDGO nameFDR corrected p-value
GO:0016998cell wall catabolic process0.00339985870717061
GO:0007047cell wall organization and biogenesis0.00339985870717061
GO:0010382cell wall metabolic process0.00339985870717061
GO:0045229external encapsulating structure organization and biogenesis0.00339985870717061
GO:0006979response to oxidative stress0.0148357470858354



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
epithelial cell2.08e-10254
kidney tubule cell5.77e-0812
nephron tubule epithelial cell5.77e-0812
endodermal cell6.51e-0859
embryonic stem cell1.39e-075
kidney cell3.70e-0718
kidney epithelial cell3.70e-0718
Uber Anatomy
Ontology termp-valuen
trunk region element6.30e-12107
abdomen element4.09e-1155
abdominal segment element4.09e-1155
immaterial anatomical entity1.81e-10126
subdivision of trunk6.67e-10113
abdominal segment of trunk6.95e-1061
abdomen6.95e-1061
duct2.48e-0926
kidney2.73e-0927
kidney mesenchyme2.73e-0927
kidney rudiment2.73e-0927
kidney field2.73e-0927
cavitated compound organ3.57e-0932
subdivision of digestive tract2.90e-08129
endodermal part of digestive tract2.90e-08129
renal tubule5.77e-0812
nephron tubule5.77e-0812
nephron tubule epithelium5.77e-0812
renal system1.86e-0745
digestive system3.34e-07155
digestive tract3.34e-07155
primitive gut3.34e-07155
epithelial sac3.84e-0725
anatomical space4.04e-07104
multi-tissue structure5.68e-07347
mesonephros6.17e-0718
pronephros6.17e-0718
nephrogenic cord6.17e-0718
pronephric mesoderm6.17e-0718
rostral part of nephrogenic cord6.17e-0718
presumptive pronephric mesoderm6.17e-0718
urinary system structure6.83e-0744
Disease
Ontology termp-valuen
carcinoma3.06e-14106
cell type cancer1.28e-10143
adenocarcinoma2.94e-1025


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
BCL11A#53335214.18472755180350.007108328585298740.0296196428790303
CTBP2#1488231.35850016966410.001492676882047230.0095394493259167
ESR1#2099215.38430164807720.006065572629693510.0268367862686956
HNF4A#3172211.56614518147680.01057585681762490.0390666682055647
NANOG#79923214.62238924050630.006698757715363760.0284846527842871



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.