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Coexpression cluster:C4308: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662038249575315!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032167739594762!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463863691131403!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154558195879282!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392500435505252!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123146933369496!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187088106529747!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295403231409937!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024640803726156!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165650676241706!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247309259280539!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155162322932409!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190864966542929
|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662038249575315!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032167739594762!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463863691131403!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154558195879282!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392500435505252!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123146933369496!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187088106529747!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295403231409937!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024640803726156!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165650676241706!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247309259280539!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155162322932409!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190864966542929
|tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.0172144,0.03272,0.0257057,0.139423,0.00229455,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.00920475,0.081977,0.0948982,0.0415721,0.0250931,0.0236364,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.0124568,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.00056041,0.00407722,0.182599,0.000584565,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.00215071,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.0223702,0.155998,0.596561,0.0693171,0.0988228,0.0842275,1.01382e-05,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.00033709,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.000770586,0.107242,0.201859,0.0695832,0.21774,0.001958,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.059488,0.0381789,0.0691572,0.268011,0.20128,0.000443992,0.807281,0.335423,0.00355277,0.261553,0.118991,0.373681,0.309233,0.49143,0.0619618,0.395854,0.00791734,0.0078057,0.0164332,0.271958,0.292154,0.0964816,0.0921263,3.66238e-07,5.1852e-06,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.0173702,0.484505,0.253571,0.276829,0.301787,0.481778,0.0565541,0.223503,0.503224,0.0026262,0.283727,0.000629694,0.00194826,0.291709,0.120054,0.212757,0.102333,0.292835,0.476744,0.439556,0.373868,0.213592,0.608919,0.18237,0.706298,0.248484,0.400457,0.275351,0.236471,0.185661,0.346319,0.535598,0.0405716,0.0772647,0.503058,0.513852,0.0389686,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.0121151,0.412837,0.671377,0.546839,0.000186789,0.448039,0.218623,0.0550136,0.00743804,0.0451077,0.0747529,7.98829e-06,0.650179,0.589326,0.50215,0.294698,0.00907354,0.138202,0.289204,0.327108,0.109738,0.00452305,0.229008,0.00262586,0.0282539,0.336314,0.19763,0.15631,0.0530502,0.104858,0.00466824,0.420626,0.516462,0.858756,0.335105,0.144809,0.145539,0.385517,0.376191,0.0224279,0.459928,0.00329638,0.152681,0.0465712,0.137098,0.0369524,0.134788,0.0985856,0.00133722,0.048108,0.284593,0.343734,0.306556,0.0524121,0.00257275,0.0340602,0.00100376,0.00488238,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.130283,0.753577,0.206222,0.03988,0.0905337,0.113671,0.040018,0.0654598,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.171389,0.257493,0.0688327,0.182325,0.34988,0.136757,0.404569,0.0847452,0.262389,0.316179,0.0697683,0.0556835,0.0198561,0.0779981,3.32302e-05,0.144322,0.223391,0.203656,0.116981,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,1.13138e-05,0.0179103,0.0517437,0.279795,0.0140073,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.00220026,0.107043,0.0419304,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0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}}
}}

Revision as of 16:40, 26 November 2012


Full id: C4308_Hepatocyte_gastrointestinal_anaplastic_liver_hepatocellular_smallcell_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr3:184095923..184095953,-p1@THPO
Hg19::chr3:184095972..184095983,-p3@THPO
Hg19::chr3:184095989..184096000,-p2@THPO


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><br>


Cell Type
Ontology termp-valuen
metabolising cell2.38e-1712
endopolyploid cell2.38e-1712
parenchymal cell2.38e-1712
polyploid cell2.38e-1712
hepatocyte2.38e-1712
endodermal cell8.99e-0758
Uber Anatomy
Ontology termp-valuen
liver1.80e-1619
digestive gland1.80e-1619
liver bud1.80e-1619
hepatic diverticulum6.39e-1422
liver primordium6.39e-1422
digestive tract diverticulum3.22e-1323
epithelial sac5.51e-1225
epithelium of foregut-midgut junction5.51e-1225
anatomical boundary5.51e-1225
hepatobiliary system5.51e-1225
foregut-midgut junction5.51e-1225
septum transversum5.51e-1225
abdomen element5.68e-1254
abdominal segment element5.68e-1254
sac1.93e-1126
endocrine gland2.67e-1135
abdominal segment of trunk2.19e-1060
abdomen2.19e-1060
endocrine system9.94e-1045
exocrine gland3.01e-0931
exocrine system3.01e-0931
gut epithelium6.73e-0954


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
CHD2#1106310.34402283411690.0009033701102746880.00662038249575315
EGR1#195834.988179094810140.008056488137383440.032167739594762
ELF1#199734.258097958807540.01295179875054610.0463863691131403
GABPB1#255337.067683836182170.002832212825417420.0154558195879282
HDAC2#3066313.41562023662630.0004140761399857210.00392500435505252
HNF4A#3172323.13229036295378.07584663437677e-050.00123146933369496
MAX#414936.452555509007120.003721913834265510.0187088106529747
MYC#460935.22228187160940.007020843755740150.0295403231409937
NFYB#4801316.75979325353650.0002123649923296180.0024640803726156
RXRA#6256320.07461713913330.0001235730348432220.00165650676241706
SP1#666735.69838137814090.005403962701712170.0247309259280539
STAT1#6772320.70658749719920.0001125992441046670.00155162322932409
USF1#739136.361499277207960.00388404057290560.0190864966542929



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.