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Coexpression cluster:C1262: Difference between revisions

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|full_id=C1262_renal_clear_Renal_papillotubular_embryonic_mucinous_serous
|full_id=C1262_renal_clear_Renal_papillotubular_embryonic_mucinous_serous
|id=C1262
|id=C1262
|ontology_enrichment_celltype=CL:0000066!5.84e-14!254;CL:1000497!1.04e-13!18;CL:0002518!1.04e-13!18;CL:1000449!1.14e-11!16;CL:1000507!2.03e-10!12;CL:1000494!2.03e-10!12;CL:0002681!1.05e-08!13;CL:0002584!1.05e-08!13;CL:0000839!4.88e-07!70;CL:0000557!8.25e-07!71
|ontology_enrichment_celltype=CL:1000497!1.42e-22!17;CL:0002518!1.42e-22!17;CL:0000066!2.43e-22!253;CL:1000507!7.33e-21!10;CL:1000494!7.33e-21!10;CL:1000449!9.66e-19!15;CL:0002681!4.12e-13!12;CL:0002584!4.12e-13!12;CL:0002149!2.19e-09!6;CL:0002255!2.19e-09!6;CL:0002274!4.52e-09!5;CL:0000457!4.52e-09!5;CL:0002191!4.52e-09!5;CL:0000097!4.52e-09!5;CL:0000831!4.52e-09!5;CL:0002028!4.52e-09!5;CL:0000223!3.47e-08!58;CL:0000239!2.97e-07!3;CL:1000615!2.97e-07!3;CL:0002306!2.97e-07!3;CL:0000163!7.65e-07!9
|ontology_enrichment_disease=DOID:305!8.55e-22!106;DOID:0050687!1.28e-19!143;DOID:162!3.13e-12!235;DOID:14566!2.00e-11!239;DOID:299!3.94e-09!25
|ontology_enrichment_disease=DOID:305!5.99e-34!106;DOID:0050687!5.66e-32!143;DOID:162!1.28e-21!235;DOID:14566!8.57e-21!239;DOID:299!7.52e-16!25;DOID:3001!2.19e-09!6;DOID:0050686!3.55e-07!137;DOID:3908!3.86e-07!5
|ontology_enrichment_uberon=UBERON:0000058!3.31e-13!26;UBERON:0002113!6.37e-13!27;UBERON:0003918!6.37e-13!27;UBERON:0005095!6.37e-13!27;UBERON:0007687!6.37e-13!27;UBERON:0004211!1.14e-11!16;UBERON:0001285!1.14e-11!16;UBERON:0007684!1.14e-11!16;UBERON:0003220!1.14e-11!16;UBERON:0004208!1.14e-11!16;UBERON:0000489!4.18e-11!32;UBERON:0005177!4.66e-11!107;UBERON:0000062!7.81e-11!511;UBERON:0006555!1.11e-10!17;UBERON:0005103!1.11e-10!17;UBERON:0000083!1.11e-10!17;UBERON:0009201!1.11e-10!17;UBERON:0004819!1.11e-10!17;UBERON:0006553!1.11e-10!17;UBERON:0003074!1.11e-10!17;UBERON:0003060!1.11e-10!17;UBERON:0009773!2.03e-10!12;UBERON:0001231!2.03e-10!12;UBERON:0004810!2.03e-10!12;UBERON:0000926!2.53e-10!448;UBERON:0004120!2.53e-10!448;UBERON:0006603!2.53e-10!448;UBERON:0005172!3.36e-10!55;UBERON:0005173!3.36e-10!55;UBERON:0006554!5.47e-10!44;UBERON:0000080!8.31e-10!18;UBERON:0002120!8.31e-10!18;UBERON:0004875!8.31e-10!18;UBERON:0005721!8.31e-10!18;UBERON:0005754!8.31e-10!18;UBERON:0007297!8.31e-10!18;UBERON:0001008!1.43e-09!45;UBERON:0003886!3.37e-09!63;UBERON:0001225!1.05e-08!13;UBERON:0008987!1.05e-08!13;UBERON:0000466!1.26e-08!126;UBERON:0000353!1.74e-08!17;UBERON:0004876!2.43e-08!20;UBERON:0002417!3.17e-08!61;UBERON:0000916!3.17e-08!61;UBERON:0001851!8.30e-08!16;UBERON:0003887!1.02e-07!21;UBERON:0001737!2.09e-07!9;UBERON:0002294!2.16e-07!7;UBERON:0001173!2.16e-07!7;UBERON:0004912!2.16e-07!7;UBERON:0000922!2.38e-07!612;UBERON:0002553!2.80e-07!70;UBERON:0000464!2.90e-07!104;UBERON:0003064!3.05e-07!37;UBERON:0004921!4.61e-07!129;UBERON:0004185!4.61e-07!129;UBERON:0002108!6.03e-07!14;UBERON:0000923!7.63e-07!604;UBERON:0005291!7.63e-07!604;UBERON:0006598!7.63e-07!604;UBERON:0002532!7.63e-07!604;UBERON:0002050!9.23e-07!605;UBERON:0005423!9.23e-07!605
|ontology_enrichment_uberon=UBERON:0004810!7.33e-21!10;UBERON:0004211!9.66e-19!15;UBERON:0009773!9.66e-19!15;UBERON:0001231!9.66e-19!15;UBERON:0001285!9.66e-19!15;UBERON:0007684!9.66e-19!15;UBERON:0004208!9.66e-19!15;UBERON:0005177!6.69e-18!101;UBERON:0002113!1.58e-17!26;UBERON:0003918!1.58e-17!26;UBERON:0011143!1.58e-17!26;UBERON:0005095!1.58e-17!26;UBERON:0007687!1.58e-17!26;UBERON:0006555!2.31e-17!16;UBERON:0004819!2.31e-17!16;UBERON:0000489!5.33e-16!31;UBERON:0001225!4.12e-13!12;UBERON:0008987!4.12e-13!12;UBERON:0005172!1.58e-12!54;UBERON:0005173!1.58e-12!54;UBERON:0001851!2.48e-12!15;UBERON:0000353!3.59e-12!15;UBERON:0006554!1.34e-11!47;UBERON:0001008!3.02e-11!48;UBERON:0002417!1.12e-10!60;UBERON:0000916!1.12e-10!60;UBERON:0002075!4.99e-10!18;UBERON:0001264!6.47e-10!10;UBERON:0000058!6.79e-09!19;UBERON:0002100!9.94e-09!199;UBERON:0002294!1.02e-07!9;UBERON:0001173!1.02e-07!9;UBERON:0004912!1.02e-07!9;UBERON:0000466!1.09e-07!117;UBERON:0009569!1.43e-07!112;UBERON:0006853!2.97e-07!3;UBERON:0007685!2.97e-07!3;UBERON:0004134!2.97e-07!3;UBERON:0003886!4.84e-07!54;UBERON:0000062!5.36e-07!503
|tf_chipseq_enrich=POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223541951648695!TFAP2C#7022;7:10.8092286098602:5.79365976833206e-08:3.61244198534228e-06
|tf_chipseq_enrich=POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223541951648695!TFAP2C#7022;7:10.8092286098602:5.79365976833206e-08:3.61244198534228e-06
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0.146629,0.426032,0.440859,0.177111,0.167984,0.337564,0.394053,0.123448,0.17256,0.126216,0.0947479,0.0787488,0.0883646,0.000717531,0.353144,0.0974692,0.11039,0.361507,0.660283,0.0754745,0.632378,0.439214,0.0896836,0.133679,0.135599,0.262768,0.235824,0.23812,0.506939,0.0654706,0.844302,3.95461e-05,0.0883079,0.192275,0.123717,0.3044,0.494788,0.435034,0.388488,0.27954,0.689314,0.468189,0.545823,0.0151026,0.35711,0.180717,0.00140837,0.0717099,0.311267,0.299453,0.347601,0.297851,0.195385,0.578705,0.000172001,0.106912,0.207535,0.747423,0.283013,0.17144,0.236468,0.274647,0.280244,5.67673e-06,2.10875e-06,0.1168,0.216736,0.112879,0.138362,0.1674,0.205022,0.304414,0.0775871,0.1646,0.530976,0.000108924,0.239252,0.435374,0.190081,0.25636,0.392755,0.366993,0.28337,0.12921,0.107541,0.00129214,0.136306,0.362226,0.0016923,0.158567,0.446426,0.551931,0.0810658,0.0399122,0.361819,0.000785211,0.00103033,0.417001,0.00287672,0.0299741,0.150144,0.235575,0.111506,0.209512,0.415762,0.167545,0.1033,0.238509,0.156356,0.450242,0.322099,0.0857464,0.282499,0.101873,0.121306,0.246526,0.203595,0.356991,0.00237982,0.116879,0.128341,0.463619,0.168391,0.545636,0.320047,0.397073,0.437057,0.221207,0.603174,0.0104433,0.621995,0.318595,0.140173,0.390753,0.312917,0.487534,0.326484,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.325012,0.353123,0.394821,0.291345,0.0235357,0.491263,0.547467,0.255995,0.184894,0.609179,0.244347,0.243363,0.382464,0.361244,0.207462,0.51104,0.487422,0.29768,0.217499,0.500934,0.225368,0.244195,0.0586175,0.348776,0.198885,0.608664,0.347052,0.386025,0.1797,0.379465,0.327304,0.0121237,0.00171731,0.132491,0.48467,0.367752,0.436987,0.458334,0.704893,0.000123893,0.0821811,0.71056,0.279549,0.0984834,0.284421,0.71736,0.000129741,0.751141,0.704995,0.458949,0.00286474,0.741039,0.659829,0.726427,0.40466,0.401507,0.330231,0.648881,0.00815518,0.103532,0.330529,0.00340856,0.045113,0.0329228,0.684866,5.82431e-06,4.98648e-05,0.0129614,0.822139,2.29711e-07,0.00137887,0.451787,0.0940476,0.00826896,0.000184614,0.542303,0.0259335,0.558605,0.0129706,0.54891,0.341975,0.765292,0.188404,0.863925,0.780774,0.0724603,0.184791,0.501908,0.161783,0.478352,0.00334811,0.685599,9.59122e-05,0.00637715,0.337191,0.00195,0.434172,0.797881,0.00526799,0.664234,0.00393016,0.446842,1.60374e-09,0.398911,0.00299684,0.411785,0.40673,0.415502,0.565657,0.499305,0.726141,0.632958,0.676266,0.327011,0.299176,0.129041,0.210121,0.585578,1.36295e-07,0.341296,0.457524,0.258349,0.00834452,0.0464251,0.585566,0.373172,0.000154475,0.000313932,2.2867e-05,0.706206,0.241641,0.596462,0.000269402,0.619962,0.377003,0.316667,0.821879,0.32842,0.268974,0.000354185,0.715629,0.715255,0.00378415,2.21918e-05,0.0545685,2.05841e-05,0.0543219,0.294507,0.017546,0.346938,0.40211,0.183851,4.36345e-06,4.82794e-06,0.362009,0.00287953,0.0978366,0.516101,0.706724,0.0919405,0.265466,0.685486,0.651111,0.466416,0.411899,0.525367,0.300829,2.46861e-07,0.0195444,0.528332,0.421737,0.573415,0.474724,0.661532,0.0113311,0.570287,0.797742,0.00116042,0.808962,0.490466,0.0278425,0.057009,0.0259208,0.0212266,0.00164237,0.400622,0.391073,0.766374,2.82164e-06,0.21176,0.057938,0.0442782,0.30566,0.775603,0.00749493,0.525188,0.000844968,0.173588,0.67786,0.0193704,0.278413,0.620377,0.00193853,0.00722451,0.680876,0.000441082,1.555e-05,0.564763,0.904403,0.0173078,0.364157,0.172412,0.0413582,0.00225133,0.0769041,0.387804,0.155446,0.385339,0.159832,0.162096,0.065336,0.390233,0.0657095,0.438999,0.103879,0.197678,0.208523,0.00926957,0.4924,0.670197,0.497662,0.418843,0.402298,0.369586,0.394729,0.441472,0.444932,0.622992,0.215866,0.436618,0.0952884,0.382758,0.264429,0.404954,0.0744027,0.204325,0.265849,0.370442,0.122027,0.533438,0.188364,0.279598,0.0180486,0.029882,0.0218266,0.150111,0.420451,0.514853,0.244241,0.0530412,0.023925,0.3382,0.454846,0.350305,0.0875262,0.147486,0.0002971,0.103076,0.0379321,0.40865,0.266737,0.00072606,0.0366694,0.215261,0.235004,1.56664e-05,0.0200356,0.331422,0.440492,0.397558,0.266168,0.0343145,0.57634,0.371725,0.334024,0.033423,0.316975,0.0203584,0.26559,0.378345,0.380153,0.160696,0.502341,0.507413,0.412407,0.42955,0.418893,0.300222,0.393729,0.487504,0.249956,0.447581,0.482721,0.0104513,0.406625,0.296254,0.400859,0.027448,0.327684,0.279523,0.499937,0.444635,0.356463,0.364875,0.211724,0.409573,0.215534,0.180313,0.436872,0.181464,0.40945,0.231548,0.120636,0.121001,0.0568736,0.172653,0.0924531,0.120918,0.0134395,6.52885e-08,0.000274835,0.0132872,0.128819,0.0873107,0.179489,0.214126,0.143317,0.261663,0.14273,0.00235668,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.197757,0.0457544,0.630108,0.299959,0.160183,0.152289,0.0966304,0.452427,2.60668e-06,0.000700753,0.0772865,0.540845,0.511559,0.280842,0.335456,0.416632,0.404559,0.0013284,0.467154,0.065788,0.249647,0.0206178,0.446356,0.248584,0.092053,0.390152,0.537963,0.540199,5.63358e-07,0.0669229,0.447064,0.20487,0.23711,0.449548,0.41929,0.209566,0.189123,0.588995,0.355645,0.332105,0.0389799,0.158122,0.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}}
}}

Revision as of 11:03, 19 October 2012


Full id: C1262_renal_clear_Renal_papillotubular_embryonic_mucinous_serous



Phase1 CAGE Peaks

Hg19::chr22:30653345..30653353,-p@chr22:30653345..30653353
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Hg19::chr22:30653384..30653392,-p@chr22:30653384..30653392
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Hg19::chr22:30653399..30653414,-p@chr22:30653399..30653414
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Hg19::chr22:30653425..30653444,-p@chr22:30653425..30653444
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Hg19::chr22:30653669..30653690,-p@chr22:30653669..30653690
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Hg19::chr22:30653699..30653718,-p@chr22:30653699..30653718
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Hg19::chr22:30653761..30653772,-p@chr22:30653761..30653772
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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
nephron tubule epithelium7.33e-2110
nephron epithelium9.66e-1915
renal tubule9.66e-1915
nephron tubule9.66e-1915
nephron9.66e-1915
uriniferous tubule9.66e-1915
nephrogenic mesenchyme9.66e-1915
trunk region element6.69e-18101
kidney1.58e-1726
kidney mesenchyme1.58e-1726
upper urinary tract1.58e-1726
kidney rudiment1.58e-1726
kidney field1.58e-1726
excretory tube2.31e-1716
kidney epithelium2.31e-1716
cavitated compound organ5.33e-1631
cortex of kidney4.12e-1312
renal parenchyma4.12e-1312
abdomen element1.58e-1254
abdominal segment element1.58e-1254
cortex2.48e-1215
parenchyma3.59e-1215
urinary system structure1.34e-1147
renal system3.02e-1148
abdominal segment of trunk1.12e-1060
abdomen1.12e-1060
viscus4.99e-1018
pancreas6.47e-1010
duct6.79e-0919
trunk9.94e-09199
biliary system1.02e-079
biliary tree1.02e-079
biliary bud1.02e-079
immaterial anatomical entity1.09e-07117
subdivision of trunk1.43e-07112
renal cortex tubule2.97e-073
region of nephron tubule2.97e-073
proximal tubule2.97e-073
body cavity precursor4.84e-0754
organ5.36e-07503
Disease
Ontology termp-valuen
carcinoma5.99e-34106
cell type cancer5.66e-32143
cancer1.28e-21235
disease of cellular proliferation8.57e-21239
adenocarcinoma7.52e-1625
female reproductive endometrioid cancer2.19e-096
organ system cancer3.55e-07137
non-small cell lung carcinoma3.86e-075


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
POLR2A#543072.147453176558070.004747636447610280.0223541951648695
TFAP2C#7022710.80922860986025.79365976833206e-083.61244198534228e-06



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1262&oldid=2247232"