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Coexpression cluster:C2229: Difference between revisions

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|full_id=C2229_Amniotic_Placental_lung_thyroid_kidney_Small_testicular
|full_id=C2229_Amniotic_Placental_lung_thyroid_kidney_Small_testicular
|id=C2229
|id=C2229
|ontology_enrichment_celltype=CL:0000066!8.93e-32!254;CL:0002076!1.92e-19!43;CL:0000223!2.13e-18!59;CL:0002368!5.46e-10!13;CL:0002251!5.37e-08!21;CL:0002202!3.02e-07!9;CL:0002632!3.02e-07!9
|ontology_enrichment_celltype=CL:0000066!2.54e-32!253;CL:0002076!1.81e-21!42;CL:0000223!2.98e-21!58;CL:0002368!5.47e-12!13;CL:1000507!7.38e-10!10;CL:1000494!7.38e-10!10;CL:0002251!6.08e-09!20;CL:0002202!9.71e-09!9;CL:0002632!9.71e-09!9;CL:1000449!5.15e-07!15
|ontology_enrichment_disease=DOID:305!4.35e-19!106;DOID:0050687!1.12e-11!143;DOID:1749!2.05e-07!14
|ontology_enrichment_disease=DOID:305!7.50e-22!106;DOID:0050687!1.38e-13!143;DOID:1749!9.84e-09!14;DOID:299!9.16e-07!25
|ontology_enrichment_uberon=UBERON:0004119!3.76e-25!169;UBERON:0000925!3.76e-25!169;UBERON:0006595!3.76e-25!169;UBERON:0000077!3.19e-20!130;UBERON:0001007!1.42e-18!155;UBERON:0001555!1.42e-18!155;UBERON:0007026!1.42e-18!155;UBERON:0000466!4.46e-18!126;UBERON:0004921!6.32e-18!129;UBERON:0004185!6.32e-18!129;UBERON:0000464!1.03e-17!104;UBERON:0005177!6.88e-17!107;UBERON:0000481!2.53e-16!347;UBERON:0001041!8.84e-16!98;UBERON:0001004!1.02e-15!72;UBERON:0000065!4.93e-14!53;UBERON:0008947!1.42e-13!38;UBERON:0003258!1.42e-13!38;UBERON:0003104!1.67e-13!238;UBERON:0009142!1.67e-13!238;UBERON:0005911!3.05e-12!82;UBERON:0005178!4.14e-12!34;UBERON:0002224!4.14e-12!34;UBERON:0001008!9.62e-12!45;UBERON:0006554!1.59e-11!44;UBERON:0001048!1.62e-11!168;UBERON:0005181!1.93e-11!35;UBERON:0000063!9.39e-11!97;UBERON:0005153!1.19e-10!37;UBERON:0009569!1.45e-10!113;UBERON:0000922!2.09e-10!612;UBERON:0000072!5.95e-10!46;UBERON:0000062!6.84e-10!511;UBERON:0005157!1.00e-08!51;UBERON:0000058!1.87e-08!26;UBERON:0002050!1.95e-08!605;UBERON:0005423!1.95e-08!605;UBERON:0007196!2.29e-08!14;UBERON:0001558!2.29e-08!14;UBERON:0000064!3.27e-08!219;UBERON:0000475!3.74e-08!365;UBERON:0000923!3.95e-08!604;UBERON:0005291!3.95e-08!604;UBERON:0006598!3.95e-08!604;UBERON:0002532!3.95e-08!604;UBERON:0000468!4.13e-08!659;UBERON:0002553!7.00e-08!70;UBERON:0002048!7.25e-08!22;UBERON:0000117!7.25e-08!22;UBERON:0000171!7.25e-08!22;UBERON:0000170!7.25e-08!22;UBERON:0005597!7.25e-08!22;UBERON:0000118!7.25e-08!22;UBERON:0002100!8.21e-08!216;UBERON:0003064!1.58e-07!37;UBERON:0000489!2.46e-07!32;UBERON:0002113!2.94e-07!27;UBERON:0003918!2.94e-07!27;UBERON:0005095!2.94e-07!27;UBERON:0007687!2.94e-07!27;UBERON:0000915!5.12e-07!52;UBERON:0003101!6.14e-07!22;UBERON:0000079!6.14e-07!22;UBERON:0000080!6.60e-07!18;UBERON:0002120!6.60e-07!18;UBERON:0004875!6.60e-07!18;UBERON:0005721!6.60e-07!18;UBERON:0005754!6.60e-07!18;UBERON:0007297!6.60e-07!18
|ontology_enrichment_uberon=UBERON:0004119!1.64e-19!160;UBERON:0000925!1.64e-19!160;UBERON:0006595!1.64e-19!160;UBERON:0006554!1.20e-15!47;UBERON:0005177!3.87e-15!101;UBERON:0001008!4.57e-15!48;UBERON:0004921!2.64e-14!118;UBERON:0001007!3.10e-14!145;UBERON:0001555!3.10e-14!145;UBERON:0007026!3.10e-14!145;UBERON:0001041!2.05e-13!87;UBERON:0001004!2.63e-12!74;UBERON:0005911!2.75e-12!82;UBERON:0000466!2.84e-12!117;UBERON:0000065!2.06e-11!54;UBERON:0000464!4.05e-11!95;UBERON:0008947!8.83e-11!38;UBERON:0003258!8.83e-11!38;UBERON:0005153!2.24e-10!37;UBERON:0004810!7.38e-10!10;UBERON:0000481!8.94e-10!342;UBERON:0000489!1.07e-09!31;UBERON:0002113!2.42e-09!26;UBERON:0003918!2.42e-09!26;UBERON:0011143!2.42e-09!26;UBERON:0005095!2.42e-09!26;UBERON:0007687!2.42e-09!26;UBERON:0009569!2.49e-09!112;UBERON:0000062!4.18e-09!503;UBERON:0000475!4.38e-09!264;UBERON:0005178!5.94e-09!34;UBERON:0002224!5.94e-09!34;UBERON:0005181!1.71e-08!35;UBERON:0011216!2.12e-08!223;UBERON:0000477!3.83e-08!373;UBERON:0001048!4.08e-08!160;UBERON:0006555!8.17e-08!16;UBERON:0004819!8.17e-08!16;UBERON:0000922!9.13e-08!592;UBERON:0002048!1.08e-07!22;UBERON:0000117!1.08e-07!22;UBERON:0000171!1.08e-07!22;UBERON:0000170!1.08e-07!22;UBERON:0005597!1.08e-07!22;UBERON:0000118!1.08e-07!22;UBERON:0003101!1.87e-07!22;UBERON:0000079!1.87e-07!22;UBERON:0000072!2.75e-07!47;UBERON:0004211!5.15e-07!15;UBERON:0009773!5.15e-07!15;UBERON:0001231!5.15e-07!15;UBERON:0001285!5.15e-07!15;UBERON:0007684!5.15e-07!15;UBERON:0004208!5.15e-07!15;UBERON:0003135!5.70e-07!11;UBERON:0000468!7.74e-07!656
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00816122411210261!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.59415020656791e-05!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.00062580264660201!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.32275263891756e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000441999967352229!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129135557827803!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321479404935213!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243656242885324!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.00032619771861878!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114421898813688
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00816122411210261!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.59415020656791e-05!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.00062580264660201!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.32275263891756e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000441999967352229!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129135557827803!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321479404935213!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243656242885324!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.00032619771861878!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114421898813688
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118999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.0339332,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.0277507,0.460406,0.0438521,0.435508,0.0439557,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.0757944,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.20386,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,2.73495e-09,0.0451012,0.0976639,0.351199,0.833813,0.415079,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.0278785,0.00147405,0.0939463,0.286748,0.00128218,0.0471607,0.163865,0.226359,0.960445,0.709625,0.265324,0.043404,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,1.08812e-10,0.0826805,0.246601,0.193021,0.240896,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.0475113,0.320355,0.364334,0.15547,0.110256,0.000238291,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.00966571,0.147842,0.0339286,0.217363,0.119015,0.00709584,0.21618,0.000201473,0.107021,0.000185372,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.1267,0.00137171,0.502211,0.000478378,0.649813,0.537932,0.459994,0.523209,0.0465928,0.25423,0.490559,0.00332016,0.00559995,0.0272171,0.685908,0.00294638,0.0074346,0.818701,0.483077,0.590496,0.603763,0.184287,7.66752e-05,0.000629457,0.293249,0.0470729,0.0757071,0.00208746,0.478691,0.360199,0.0153629,0.657141,0.00893555,0.365494,0.212703,0.56318,0.0110532,0.315494,0.000282658,0.104625,0.0108102,0.328518,0.545608,0.310552,0.594773,0.483764,0.00961647,0.784052,0.209437,0.0118712,0.748403,0.0651244,0.169076,0.464001,0.60737,0.579004,0.150592,0.113944,0.586133,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.0205071,4.1712e-07,0.202522,6.0346e-05,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.073225,0.017253,0.721266,0.50338,0.0746831,0.404625,0.416164,0.424691,0.00931622,0.00452282,0.62689,0.00176979,0.00068395,0.284496,0.512545,0.512178,0.563206,0.260945,0.684899,0.263302,0.552023,0.180735,0.189249,0.216102,0.0355932,6.89796e-06,0.397869,0.0585759,0.226491,0.417131,0.463987,0.0782409,0.503881,0.124057,0.0202528,0.0295677,0.00339209,0.000519892,0.261657,0.346776,0.000485493,0.00866064,0.438176,0.349112,0.391754,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,6.09746e-05,0.000445343,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.12664,0.387134,0.559969,0.358813,0.303004,0.0113028,0.493455,0.346636,0.457747,0.348802,0.137708,0.579645,0.447581,0.42505,0.254628,0.131374,0.0286377,0.416962,0.632833,0.0828233,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.000690216,0.0265924,0.325254,0.266651,0.0460393,0.231754,0.249415,0.283107,0.285648,0.0191181,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.00106183,0.112422,0.170886,0.267687,0.315656,0.284866,2.88674e-06,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.0136966,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.000563201,0.202977,4.4199e-05,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.000372103,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.0154764,0.332746,0.271338,0.00288876,0.00571761,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0120454,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.00844265,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,1.27729e-11,0.151361,0.279606,0.00499935,0.150674,0.251128,0.246177,0.35674,0.0104945,0.000664446,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.00218951,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}}
}}

Revision as of 12:12, 19 October 2012


Full id: C2229_Amniotic_Placental_lung_thyroid_kidney_Small_testicular



Phase1 CAGE Peaks

Hg19::chr12:6485300..6485325,-p5@SCNN1A
Hg19::chr12:6485336..6485354,-p4@SCNN1A
Hg19::chr12:6485371..6485382,-p11@SCNN1A
Hg19::chr12:6485398..6485410,-p12@SCNN1A


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
endoderm-derived structure1.64e-19160
endoderm1.64e-19160
presumptive endoderm1.64e-19160
urinary system structure1.20e-1547
trunk region element3.87e-15101
renal system4.57e-1548
subdivision of digestive tract2.64e-14118
digestive system3.10e-14145
digestive tract3.10e-14145
primitive gut3.10e-14145
foregut2.05e-1387
respiratory system2.63e-1274
endo-epithelium2.75e-1282
immaterial anatomical entity2.84e-12117
respiratory tract2.06e-1154
anatomical space4.05e-1195
respiratory primordium8.83e-1138
endoderm of foregut8.83e-1138
epithelial bud2.24e-1037
nephron tubule epithelium7.38e-1010
multi-tissue structure8.94e-10342
cavitated compound organ1.07e-0931
kidney2.42e-0926
kidney mesenchyme2.42e-0926
upper urinary tract2.42e-0926
kidney rudiment2.42e-0926
kidney field2.42e-0926
subdivision of trunk2.49e-09112
organ4.18e-09503
organism subdivision4.38e-09264
thoracic cavity element5.94e-0934
thoracic cavity5.94e-0934
thoracic segment organ1.71e-0835
organ system subdivision2.12e-08223
anatomical cluster3.83e-08373
primordium4.08e-08160
excretory tube8.17e-0816
kidney epithelium8.17e-0816
embryo9.13e-08592
lung1.08e-0722
respiratory tube1.08e-0722
respiration organ1.08e-0722
pair of lungs1.08e-0722
lung primordium1.08e-0722
lung bud1.08e-0722
male organism1.87e-0722
male reproductive system1.87e-0722
segment of respiratory tract2.75e-0747
nephron epithelium5.15e-0715
renal tubule5.15e-0715
nephron tubule5.15e-0715
nephron5.15e-0715
uriniferous tubule5.15e-0715
nephrogenic mesenchyme5.15e-0715
male reproductive organ5.70e-0711
multi-cellular organism7.74e-07656
Disease
Ontology termp-valuen
carcinoma7.50e-22106
cell type cancer1.38e-13143
squamous cell carcinoma9.84e-0914
adenocarcinoma9.16e-0725


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
CTCF#1066445.360256373075030.001211145381643620.00816122411210261
ESR1#2099430.76860329615451.11467714392546e-064.59415020656791e-05
HDAC2#3066413.41562023662633.0859005065161e-050.00062580264660201
NANOG#79923429.24477848101271.36586687657858e-065.32275263891756e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000441999967352229
RAD21#5885410.35503389545638.6948481184721e-050.00129135557827803
TAF1#687243.343046285745290.008005664898701650.0321479404935213
TBP#690843.706770687096390.005296377814784350.0243656242885324
TFAP2A#7020416.5186343730451.34240829060362e-050.00032619771861878
TFAP2C#7022410.80922860986027.32289634782688e-050.00114421898813688



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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