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Coexpression cluster:C4464: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130253499368578!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327062272810843!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438400174932451!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323811124491528!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321997460709575!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140720345805633!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109890249469046
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130253499368578!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327062272810843!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438400174932451!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323811124491528!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321997460709575!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140720345805633!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109890249469046
|tfbs_overrepresentation=0.147255,0.0586687,9.02183e-07,0.0477154,0.199763,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.00195662,0.140982,0.0982016,0.0528514,0.108057,0.0190294,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00687964,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.00146949,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.000156996,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,2.96037e-11,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,3.42963e-08,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,5.12341e-06,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.0174119,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.00111717,0.137725,2.24466e-08,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.037005,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.00958651,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.0219021,0.0695832,3.59546e-05,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.0356268,0.119261,0.0865903,0.0380459,0.130174,0.219944,6.67011e-06,1.04397e-09,0.0821962,0.20128,4.19008e-08,2.97413e-11,6.76379e-05,0.0185583,0.261553,0.446302,0.373681,0.053682,0.49143,0.00800846,0.395854,0.00791734,0.0078057,0.000471837,0.271958,0.292154,0.405773,0.0148713,0.581713,4.6248e-05,0.187251,0.362792,0.181715,0.10624,0.109988,0.330894,0.0257868,0.427027,0.376924,0.463191,0.647576,0.528324,0.00682286,0.370782,0.101703,0.142924,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.0340949,0.0146955,0.283727,0.314747,0.000273712,0.291709,0.448095,0.0563639,0.416816,0.292835,0.00439271,0.0210941,0.0807167,0.0116572,0.0694028,0.18237,7.73889e-09,5.65743e-11,2.41966e-07,0.275351,0.236471,0.185661,0.000971103,0.179399,0.270984,0.0772647,0.0340542,0.00637776,0.522083,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,5.13222e-06,2.85971e-06,0.581837,0.412837,0.671377,0.0462094,0.551561,0.120021,0.218623,0.312808,3.44841e-05,0.0451077,0.0747529,0.0284893,1.4525e-05,0.061213,7.77418e-13,0.294698,0.34331,0.138202,0.289204,0.327108,4.0585e-08,0.278044,2.27318e-14,0.428671,0.00238478,0.336314,0.19763,0.15631,0.0530502,0.104858,0.48267,0.104399,0.516462,2.91338e-09,0.335105,0.144809,0.145539,0.385517,0.376191,0.0224279,0.127215,0.252232,0.152681,0.0465712,0.137098,0.00360191,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.000553055,0.601433,0.503082,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,2.30954e-13,0.206222,0.171685,1.79865e-07,0.00288466,0.269226,0.339277,2.13553e-05,0.281425,0.141758,0.124432,0.168058,0.0134764,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.171389,7.42877e-05,0.0688327,0.0081614,0.0699395,0.136757,0.00199596,9.61912e-05,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.116981,0.0214618,0.191777,0.111931,0.28934,0.000961869,0.303336,0.126478,0.134852,0.10689,0.000335843,0.0627924,0.00151445,0.0179103,0.0517437,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.062811,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.2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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4464_anaplastic_Prostate_esophagus_Smooth_glassy_cervical_biphenotypic



Phase1 CAGE Peaks

Hg19::chr5:134369905..134369972,-p1@PITX1
Hg19::chr5:134369973..134369984,-p3@PITX1
Hg19::chr5:134370033..134370042,-p5@PITX1


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>


Cell Type
Ontology termp-valuen
epithelial cell1.84e-20253
endo-epithelial cell2.73e-1842
endodermal cell6.39e-1858
epithelial cell of alimentary canal7.99e-1120
respiratory epithelial cell6.21e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.48e-27160
endoderm9.48e-27160
presumptive endoderm9.48e-27160
digestive system3.03e-24145
digestive tract3.03e-24145
primitive gut3.03e-24145
subdivision of digestive tract1.95e-21118
respiratory system9.56e-1674
orifice3.99e-1336
foregut7.14e-1387
respiratory tract8.98e-1254
segment of respiratory tract1.43e-1147
respiratory primordium6.70e-1138
endoderm of foregut6.70e-1138
endo-epithelium1.17e-1082
epithelial bud3.48e-0937
thoracic cavity element1.68e-0834
thoracic cavity1.68e-0834
hindgut3.30e-0819
mucosa4.52e-0820
thoracic segment organ5.48e-0835
oral opening1.04e-0722
mouth1.39e-0729
stomodeum1.39e-0729
larynx1.50e-079
cloaca5.88e-0714
anal region5.88e-0714
embryonic cloaca5.88e-0714
terminal part of digestive tract5.88e-0714
primitive urogenital sinus5.88e-0714
proctodeum5.88e-0714
Disease
Ontology termp-valuen
cancer8.58e-37235
disease of cellular proliferation1.58e-35239
cell type cancer8.21e-32143
carcinoma9.16e-31106
organ system cancer2.46e-09137
squamous cell carcinoma2.57e-0814


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
CTBP2#1488362.71700033932814.049570681927e-060.000130253499368578
E2F1#186934.907389214879320.008460985347239390.0327062272810843
E2F4#1874312.66806031528440.0004917987006298980.00438400174932451
E2F6#187635.017155731697390.00791769806886330.0323811124491528
EGR1#195834.988179094810140.008056488137383440.0321997460709575
ZBTB7A#5134137.35190930787590.002516255860282270.0140720345805633
ZNF263#1012738.221841637010680.001799043925565870.0109890249469046



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.