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Coexpression cluster:C4533: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.16e-08!106
|ontology_enrichment_disease=DOID:305!1.16e-08!106
|ontology_enrichment_uberon=UBERON:0004119!8.93e-19!169;UBERON:0000925!8.93e-19!169;UBERON:0006595!8.93e-19!169;UBERON:0001007!7.60e-16!155;UBERON:0001555!7.60e-16!155;UBERON:0007026!7.60e-16!155;UBERON:0003104!1.11e-13!238;UBERON:0009142!1.11e-13!238;UBERON:0004921!1.62e-12!129;UBERON:0004185!1.62e-12!129;UBERON:0001004!1.71e-11!72;UBERON:0000077!1.86e-11!130;UBERON:0002100!1.25e-10!216;UBERON:0000467!3.51e-10!625;UBERON:0000480!5.05e-10!626;UBERON:0000468!9.00e-10!659;UBERON:0000481!1.39e-09!347;UBERON:0003102!4.18e-09!95;UBERON:0003100!5.66e-09!41;UBERON:0000065!1.05e-08!53;UBERON:0000062!1.15e-08!511;UBERON:0000926!2.50e-08!448;UBERON:0004120!2.50e-08!448;UBERON:0006603!2.50e-08!448;UBERON:0000161!3.20e-08!35;UBERON:0000475!5.76e-08!365;UBERON:0000486!7.64e-08!82;UBERON:0008947!2.05e-07!38;UBERON:0003258!2.05e-07!38;UBERON:0003134!3.45e-07!37;UBERON:0000474!3.45e-07!37;UBERON:0000072!4.03e-07!46;UBERON:0002050!7.48e-07!605;UBERON:0005423!7.48e-07!605;UBERON:0005156!7.54e-07!59;UBERON:0000990!7.54e-07!59;UBERON:0000490!8.95e-07!138
|ontology_enrichment_uberon=UBERON:0004119!8.93e-19!169;UBERON:0000925!8.93e-19!169;UBERON:0006595!8.93e-19!169;UBERON:0001007!7.60e-16!155;UBERON:0001555!7.60e-16!155;UBERON:0007026!7.60e-16!155;UBERON:0003104!1.11e-13!238;UBERON:0009142!1.11e-13!238;UBERON:0004921!1.62e-12!129;UBERON:0004185!1.62e-12!129;UBERON:0001004!1.71e-11!72;UBERON:0000077!1.86e-11!130;UBERON:0002100!1.25e-10!216;UBERON:0000467!3.51e-10!625;UBERON:0000480!5.05e-10!626;UBERON:0000468!9.00e-10!659;UBERON:0000481!1.39e-09!347;UBERON:0003102!4.18e-09!95;UBERON:0003100!5.66e-09!41;UBERON:0000065!1.05e-08!53;UBERON:0000062!1.15e-08!511;UBERON:0000926!2.50e-08!448;UBERON:0004120!2.50e-08!448;UBERON:0006603!2.50e-08!448;UBERON:0000161!3.20e-08!35;UBERON:0000475!5.76e-08!365;UBERON:0000486!7.64e-08!82;UBERON:0008947!2.05e-07!38;UBERON:0003258!2.05e-07!38;UBERON:0003134!3.45e-07!37;UBERON:0000474!3.45e-07!37;UBERON:0000072!4.03e-07!46;UBERON:0002050!7.48e-07!605;UBERON:0005423!7.48e-07!605;UBERON:0005156!7.54e-07!59;UBERON:0000990!7.54e-07!59;UBERON:0000490!8.95e-07!138
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032728031432605!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00918502996012008!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464548701733733!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435735461975357!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157507264590792!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473030672431246!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.0013730360952667!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203841122256287!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376155801570202!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249272829520452!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618319694604458
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.00190755,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.00989266,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.0641358,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0538541,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.198118,0.635872,0.563047,0.823736,0.489965,0.0638737,0.261644,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.178727,0.0724671,0.271958,0.292154,0.405773,0.39729,0.217139,0.0643874,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.168255,0.370782,0.0173702,0.484505,0.253571,0.276829,0.301787,0.481778,0.0565541,0.223503,0.503224,0.603208,0.283727,4.69813e-05,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.346458,0.248484,0.747852,0.275351,0.0304678,0.185661,0.346319,0.535598,0.270984,0.0772647,0.503058,0.513852,0.000993751,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.0583074,0.412837,0.671377,0.546839,0.551561,0.0225539,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.0054714,0.34331,0.0282052,0.289204,0.327108,0.319027,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.104399,0.516462,0.582303,0.335105,0.144809,0.145539,0.0134194,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.0524121,0.601433,0.503082,0.0391885,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.00388249,0.753577,0.206222,0.525396,0.651524,0.437176,0.269226,0.0654598,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.0186811,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.015204,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.16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0.361435
}}
}}

Revision as of 13:04, 5 September 2012


Full id: C4533_lung_gall_rectal_salivary_Prostate_Keratinocyte_amniotic



Phase1 CAGE Peaks

Hg19::chr5:95998673..95998713,+p7@CAST
Hg19::chr5:95998714..95998744,+p5@CAST
Hg19::chr5:95998746..95998764,+p12@CAST


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
endo-epithelial cell1.81e-1543
endodermal cell8.90e-1459
epithelial cell2.45e-12254
epithelial cell of alimentary canal1.02e-0721
vascular associated smooth muscle cell6.01e-0732
embryonic cell9.87e-07248
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure8.93e-19169
endoderm8.93e-19169
presumptive endoderm8.93e-19169
digestive system7.60e-16155
digestive tract7.60e-16155
primitive gut7.60e-16155
mesenchyme1.11e-13238
entire embryonic mesenchyme1.11e-13238
subdivision of digestive tract1.62e-12129
endodermal part of digestive tract1.62e-12129
respiratory system1.71e-1172
mixed endoderm/mesoderm-derived structure1.86e-11130
trunk1.25e-10216
anatomical system3.51e-10625
anatomical group5.05e-10626
multi-cellular organism9.00e-10659
multi-tissue structure1.39e-09347
surface structure4.18e-0995
female organism5.66e-0941
respiratory tract1.05e-0853
organ1.15e-08511
mesoderm2.50e-08448
mesoderm-derived structure2.50e-08448
presumptive mesoderm2.50e-08448
orifice3.20e-0835
organism subdivision5.76e-08365
multilaminar epithelium7.64e-0882
respiratory primordium2.05e-0738
endoderm of foregut2.05e-0738
female reproductive organ3.45e-0737
female reproductive system3.45e-0737
segment of respiratory tract4.03e-0746
embryonic structure7.48e-07605
developing anatomical structure7.48e-07605
reproductive structure7.54e-0759
reproductive system7.54e-0759
unilaminar epithelium8.95e-07138
Disease
Ontology termp-valuen
carcinoma1.16e-08106


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
E2F1#186934.907389214879320.008460985347239390.032728031432605
EBF1#187938.9064668465690.00141523283560980.00918502996012008
ELF1#199734.258097958807540.01295179875054610.0464548701733733
GTF2F1#2962312.73966087675770.0004835525047438590.00435735461975357
JUND#372736.994663941871030.002921845042734990.0157507264590792
NRF1#4899312.21027944771090.0005492172401020010.00473030672431246
PBX3#5090321.91451268674419.49854535978121e-050.0013730360952667
SMARCB1#6598318.25271578115740.000164397760679890.00203841122256287
SRF#6722313.79717826216780.0003806615025800190.00376155801570202
TFAP2A#7020316.5186343730450.0002218033880766340.00249272829520452
TFAP2C#7022310.80922860986020.0007916746575753130.00618319694604458



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.