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Coexpression cluster:C3195: Difference between revisions

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|full_id=C3195_Bronchial_Prostate_Tracheal_Alveolar_iPS_Osteoblast_H9
|full_id=C3195_Bronchial_Prostate_Tracheal_Alveolar_iPS_Osteoblast_H9
|id=C3195
|id=C3195
|ontology_enrichment_celltype=CL:0002321!5.28e-21!248;CL:0000220!3.33e-20!246;CL:0000144!1.62e-18!625;CL:0000548!4.31e-18!679;CL:0000004!4.31e-18!679;CL:0000255!4.31e-18!679;CL:0000012!1.32e-17!682;CL:0002371!8.93e-16!591;CL:0002076!1.60e-11!43;CL:0000066!3.71e-11!254;CL:0002077!3.03e-10!33;CL:0000222!6.33e-09!119;CL:0000003!4.46e-08!722;CL:0000063!5.22e-08!578;CL:0000393!9.41e-08!60;CL:0000211!9.41e-08!60;CL:0000183!1.25e-07!59;CL:0000187!8.78e-07!54;CL:0000680!9.46e-07!57;CL:0000056!9.46e-07!57;CL:0000355!9.46e-07!57
|ontology_enrichment_celltype=CL:0002321!1.53e-20!250;CL:0000548!2.21e-18!679;CL:0000255!2.21e-18!679;CL:0002371!3.87e-17!588;CL:0000066!2.20e-11!253;CL:0002076!6.24e-11!42;CL:0002077!2.03e-10!34;CL:0000325!1.89e-09!87;CL:0000222!9.65e-09!121;CL:0000003!2.60e-08!722;CL:0000393!1.16e-07!61;CL:0000211!1.16e-07!61;CL:0000183!3.55e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000486!9.31e-09!82;UBERON:0001637!3.36e-08!42;UBERON:0003509!3.36e-08!42;UBERON:0004572!3.36e-08!42;UBERON:0004872!5.29e-08!84;UBERON:0000914!1.42e-07!83;UBERON:0002329!1.42e-07!83;UBERON:0003077!1.42e-07!83;UBERON:0003059!1.42e-07!83;UBERON:0007282!1.42e-07!83;UBERON:0009618!1.42e-07!83;UBERON:0007285!1.42e-07!83;UBERON:0000926!1.53e-07!448;UBERON:0004120!1.53e-07!448;UBERON:0006603!1.53e-07!448;UBERON:0001981!5.41e-07!60;UBERON:0007500!5.41e-07!60;UBERON:0004537!5.41e-07!60;UBERON:0006965!5.41e-07!60;UBERON:0004290!5.41e-07!70;UBERON:0000055!7.07e-07!69;UBERON:0000922!7.38e-07!612
|ontology_enrichment_uberon=UBERON:0000926!1.32e-08!315;UBERON:0004120!1.32e-08!315;UBERON:0006603!1.32e-08!315;UBERON:0004872!1.68e-08!83;UBERON:0007503!2.02e-08!78;UBERON:0000486!2.48e-08!83;UBERON:0001637!2.54e-08!42;UBERON:0003509!2.54e-08!42;UBERON:0004572!2.54e-08!42;UBERON:0000468!2.31e-07!656;UBERON:0000922!2.80e-07!592;UBERON:0007500!3.32e-07!59;UBERON:0001981!3.32e-07!59;UBERON:0004537!3.32e-07!59;UBERON:0006965!3.32e-07!59;UBERON:0000055!5.90e-07!68
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460137102017303
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460137102017303
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.0172144,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.241734,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.0101452,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.0641358,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.0381183,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.355018,0.00485874,0.268011,0.20128,0.517782,0.489965,0.335423,0.261644,0.261553,0.118991,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.042539,0.0164332,0.271958,0.292154,0.405773,0.39729,0.217139,0.0643874,0.187251,0.362792,0.181715,0.0186051,0.109988,0.0620388,0.218329,0.107929,0.376924,0.129235,0.0883629,0.528324,0.03861,0.370782,0.101703,0.142924,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.155672,0.236436,0.283727,0.314747,0.0567394,0.291709,0.448095,0.00192508,0.416816,0.292835,0.476744,0.115044,0.0120909,0.213592,0.241757,0.18237,0.346458,0.821217,0.161148,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.258117,0.503058,0.513852,0.169228,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.412837,0.102184,0.546839,0.551561,0.448039,0.0258593,0.312808,0.333034,0.0451077,0.0747529,0.00241532,0.0222308,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.109738,0.278044,0.229008,0.428671,0.0282539,0.336314,0.19763,0.0129079,0.20495,0.104858,0.0293525,0.104399,0.516462,0.582303,0.335105,0.144809,0.145539,0.385517,0.0818086,0.0224279,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.503082,0.169823,0.284629,0.262537,0.359455,0.0277799,0.405955,0.102469,0.0760312,0.464871,0.0538047,0.206222,0.525396,0.284166,0.113671,0.269226,0.339277,0.0479524,0.281425,0.141758,0.124432,0.520495,0.159617,0.0310416,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.0688327,0.539392,0.34988,0.475069,0.00199596,0.0847452,0.262389,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.000432194,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.0200986,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.026047,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.0164446,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058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}}
}}

Revision as of 14:53, 19 October 2012


Full id: C3195_Bronchial_Prostate_Tracheal_Alveolar_iPS_Osteoblast_H9



Phase1 CAGE Peaks

Hg19::chr11:67352151..67352174,+p8@GSTP1
Hg19::chr11:67352177..67352212,+p5@GSTP1
Hg19::chr11:67352594..67352692,+p3@GSTP1


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
embryonic cell1.53e-20250
animal cell2.21e-18679
eukaryotic cell2.21e-18679
somatic cell3.87e-17588
epithelial cell2.20e-11253
endo-epithelial cell6.24e-1142
ecto-epithelial cell2.03e-1034
stuff accumulating cell1.89e-0987
mesodermal cell9.65e-09121
native cell2.60e-08722
electrically responsive cell1.16e-0761
electrically active cell1.16e-0761
contractile cell3.55e-0759
Uber Anatomy
Ontology termp-valuen
mesoderm1.32e-08315
mesoderm-derived structure1.32e-08315
presumptive mesoderm1.32e-08315
splanchnic layer of lateral plate mesoderm1.68e-0883
epithelial vesicle2.02e-0878
multilaminar epithelium2.48e-0883
artery2.54e-0842
arterial blood vessel2.54e-0842
arterial system2.54e-0842
multi-cellular organism2.31e-07656
embryo2.80e-07592
epithelial tube open at both ends3.32e-0759
blood vessel3.32e-0759
blood vasculature3.32e-0759
vascular cord3.32e-0759
vessel5.90e-0768


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
NR3C1#290829.982015554115360.01278474365547170.0460137102017303



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.