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Coexpression cluster:C1269: Difference between revisions

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|tf_chipseq_enrich=ZNF263#10127;6:7.04729283172344:2.02874079383503e-05:0.000450041758214393
|tf_chipseq_enrich=ZNF263#10127;6:7.04729283172344:2.02874079383503e-05:0.000450041758214393
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26032,0.440859,0.177111,0.167984,0.337564,0.394053,0.123448,0.17256,0.126216,0.0947479,0.0787488,0.0883646,0.00536092,0.353144,0.407665,0.11039,0.361507,0.660283,0.0754745,0.632378,0.114847,0.0896836,0.00936212,0.718626,0.262768,0.235824,0.23812,9.509e-05,0.0654706,9.17122e-08,0.00614914,0.0883079,0.192275,0.123717,0.0519109,0.149841,0.435034,0.388488,0.27954,0.689314,0.468189,0.545823,0.168686,0.35711,0.180717,0.375467,7.55133e-07,0.311267,0.299453,0.347601,0.297851,0.195385,2.93338e-08,0.546003,0.106912,0.207535,0.0133284,0.283013,0.17144,0.236468,0.274647,0.280244,3.24148e-08,0.164035,0.1168,0.216736,0.112879,0.138362,0.1674,0.205022,0.304414,0.0775871,0.1646,0.530976,5.67692e-06,0.013778,0.435374,0.54926,0.25636,0.392755,0.366993,0.843094,0.12921,0.107541,0.00129214,0.00974303,0.362226,0.565792,0.0132946,0.446426,0.551931,0.0810658,0.268889,0.361819,5.33882e-16,1.1713e-26,0.417001,0.436925,0.234633,0.150144,0.235575,0.111506,0.209512,0.415762,0.167545,0.1033,0.238509,0.156356,0.450242,0.322099,0.0857464,0.282499,0.101873,0.121306,0.246526,0.203595,0.356991,0.227948,0.44271,0.128341,0.463619,0.168391,1.89886e-05,0.320047,0.397073,0.0206783,0.221207,0.06691,0.358,0.621995,0.318595,0.140173,0.390753,0.312917,2.41379e-13,0.326484,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.0597011,0.353123,0.394821,0.291345,0.453507,0.491263,0.547467,0.255995,0.184894,0.609179,0.244347,0.243363,0.0848007,0.0107656,0.207462,0.51104,0.487422,0.29768,0.217499,0.500934,0.225368,0.244195,0.0586175,0.348776,0.198885,0.0577473,0.347052,0.386025,0.1797,0.379465,0.00773791,0.0121237,0.0892444,0.132491,0.0297894,0.000115449,0.0206668,0.458334,5.98869e-11,1.25634e-07,0.0821811,0.71056,0.279549,0.0984834,0.000400506,0.71736,1.71573e-05,0.751141,0.704995,0.458949,0.840587,0.391162,0.659829,0.726427,0.40466,0.401507,0.692805,0.648881,0.703424,0.673541,0.000261254,0.910041,0.732853,2.04806e-08,0.320963,0.0054033,0.221836,0.744931,0.00859285,4.8383e-10,8.42817e-09,0.451787,0.818359,0.0270901,0.680172,0.542303,1.74787e-07,0.846379,0.00420601,0.54891,0.341975,0.765292,0.547149,0.863925,0.195597,0.615729,0.0174031,0.501908,0.74852,0.478352,1.90228e-07,0.685599,9.59122e-05,5.03704e-06,0.337191,3.59096e-05,0.00346315,0.797881,2.1662e-06,0.664234,5.14969e-08,0.19467,2.48474e-07,0.00178744,7.62878e-07,0.411785,0.40673,0.415502,0.565657,8.44374e-05,0.726141,0.632958,0.676266,0.327011,0.299176,8.2573e-10,0.210121,0.585578,0.640275,0.341296,0.457524,0.258349,0.541728,0.303955,0.585566,0.373172,0.538803,7.56305e-09,0.654029,0.706206,0.505417,0.230258,0.00111158,0.619962,0.00197177,0.681127,0.821879,1.04723e-05,0.00255765,0.443364,0.715629,0.357569,0.765316,5.71964e-09,0.0545685,0.41419,0.7547,0.294507,0.000388851,0.346938,0.40211,0.183851,0.588416,0.783193,0.362009,0.611179,0.664218,0.0977719,0.706724,0.654039,0.832266,0.685486,0.283731,0.466416,0.411899,0.525367,0.667,0.748565,0.635414,0.528332,2.21217e-07,0.573415,0.474724,0.661532,0.574524,0.570287,0.00600878,0.68023,2.434e-08,0.146908,0.676249,0.760368,0.0259208,0.440345,0.027142,0.400622,0.391073,0.766374,0.883398,0.575489,0.0157471,0.540565,0.0143213,0.775603,0.695855,0.525188,0.657348,0.173588,0.312949,0.780554,0.646027,0.620377,0.402066,0.00722451,0.31638,0.610982,0.256934,0.564763,0.0894143,0.415214,0.364157,0.172412,0.53064,0.415017,0.0769041,0.387804,0.502902,0.385339,0.159832,0.512288,0.338978,0.390233,0.339879,0.438999,0.41967,0.197678,0.208523,0.34551,0.4924,0.670197,0.497662,0.418843,0.749185,0.369586,0.0145458,0.441472,0.444932,0.622992,0.580249,0.436618,0.403472,0.382758,0.264429,0.404954,0.0744027,0.204325,0.265849,0.370442,0.451398,0.533438,0.188364,0.279598,0.420279,0.485091,0.443868,0.150111,0.420451,0.514853,0.244241,0.307495,0.455626,0.3382,0.023781,0.350305,0.0875262,0.0114541,0.117583,0.00550491,0.518238,0.40865,0.634608,0.324846,0.25829,0.215261,0.235004,0.133496,0.433115,0.331422,0.440492,0.397558,0.266168,0.504119,0.0562494,0.371725,0.334024,0.500457,0.316975,0.435107,0.26559,0.378345,0.0127947,0.160696,0.502341,0.507413,0.412407,0.42955,0.103456,0.300222,0.393729,0.487504,0.249956,0.447581,0.141745,0.0104513,0.406625,0.296254,0.0939442,0.473667,0.0607565,0.279523,0.499937,0.444635,0.356463,0.364875,0.211724,0.409573,0.579867,0.536787,0.436872,0.181464,0.40945,0.231548,0.120636,0.121001,0.317719,0.172653,0.0924531,0.120918,0.593272,0.507382,0.425328,0.384398,0.462521,0.387627,0.179489,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.558766,0.545381,0.630108,0.299959,0.509613,0.152289,0.406059,0.452427,0.56256,0.494497,0.366448,0.540845,0.511559,0.280842,0.335456,0.416632,0.404559,0.545676,0.467154,0.600528,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.540199,0.488863,0.342785,0.447064,0.20487,0.0147917,0.449548,0.41929,0.209566,0.0191316,0.588995,0.355645,0.332105,0.522124,0.158122,0.0387004,0.220023,0.444217,0.363335,0.329186,0.0199744,0.493369,0.416144,0.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}}
}}

Revision as of 14:47, 26 November 2012


Full id: C1269_serous_Urothelial_clear_Gingival_Renal_choriocarcinoma_Corneal



Phase1 CAGE Peaks

Hg19::chr3:13859846..13859848,-p@chr3:13859846..13859848
-
Hg19::chr3:13921427..13921439,-p5@WNT7A
Hg19::chr3:13921455..13921496,-p2@WNT7A
Hg19::chr3:13921498..13921503,-p6@WNT7A
Hg19::chr3:13921557..13921575,-p1@WNT7A
Hg19::chr3:13921578..13921591,-p3@WNT7A
Hg19::chr3:13921594..13921601,-p4@WNT7A


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
ecto-epithelium4.37e-12104
neural tube5.63e-1256
neural rod5.63e-1256
future spinal cord5.63e-1256
neural keel5.63e-1256
telencephalon1.48e-1134
brain grey matter2.22e-1134
gray matter2.22e-1134
regional part of nervous system3.40e-1153
regional part of brain3.40e-1153
organ part9.15e-11218
cerebral hemisphere1.23e-1032
regional part of telencephalon1.98e-1032
ectoderm-derived structure3.32e-10171
ectoderm3.32e-10171
presumptive ectoderm3.32e-10171
regional part of forebrain3.99e-1041
forebrain3.99e-1041
anterior neural tube3.99e-1041
future forebrain3.99e-1041
central nervous system6.70e-1081
regional part of cerebral cortex7.82e-1022
cerebral cortex4.52e-0925
pallium4.52e-0925
neocortex1.20e-0820
brain5.54e-0868
future brain5.54e-0868
nervous system7.16e-0889
urothelium9.99e-085
neural plate3.03e-0782
presumptive neural plate3.03e-0782
neurectoderm5.68e-0786
nephron tubule epithelium6.16e-0710
Disease
Ontology termp-valuen
squamous cell carcinoma6.98e-1014


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
ZNF263#1012767.047292831723442.02874079383503e-050.000450041758214393



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.