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Coexpression cluster:C4037: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.84e-20!115;UBERON:0000475!1.47e-08!365;UBERON:0001737!5.73e-08!9;UBERON:0000481!1.42e-07!347;UBERON:0003102!1.43e-07!95
|ontology_enrichment_uberon=UBERON:0007023!9.84e-20!115;UBERON:0000475!1.47e-08!365;UBERON:0001737!5.73e-08!9;UBERON:0000481!1.42e-07!347;UBERON:0003102!1.43e-07!95
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115359548966196!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325856202035672!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.00067706067289961!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582091377066626!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107324124408571!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203310097426253!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614500993694625!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248497361589097!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616521583494953
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.00367271,0.688181,0.0429682,0.120351,0.0667043,8.23283e-08,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.00117529,0.0339971,0.0117862,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.000499822,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.000193634,0.0166632,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.00166778,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.0216297,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.0413643,0.114283,0.0400322,0.127369,0.0403542,0.0547453,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.00735999,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.00958651,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.219944,0.713218,0.782949,0.635872,0.20128,0.823736,0.807281,0.0638737,0.0790073,0.261553,0.446302,0.373681,0.053682,0.147559,0.330703,0.395854,0.000775053,0.000145293,0.0164332,0.271958,0.292154,0.405773,0.39729,0.0121013,0.597171,0.187251,0.0109219,0.181715,0.423979,0.109988,0.330894,0.0257868,0.427027,0.0124294,0.463191,0.647576,0.528324,0.520763,0.000121147,0.415647,0.484505,0.253571,0.276829,0.301787,0.00462582,0.316882,0.223503,0.00574256,0.603208,0.283727,0.314747,0.577664,0.291709,0.120054,0.576651,0.0175396,0.292835,0.476744,0.00296083,0.373868,0.000273537,0.241757,0.18237,0.706298,0.821217,0.161148,0.275351,0.236471,0.0184133,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.0389686,0.000221606,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.217247,0.412837,0.671377,0.546839,0.551561,0.0225539,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.000468976,0.0671437,0.000560159,0.289204,0.327108,0.683186,0.278044,0.807485,0.428671,0.228096,0.0642385,0.19763,0.0129079,0.567452,0.421464,0.00466824,1.77925e-06,8.10939e-08,0.858756,0.335105,0.144809,0.145539,0.385517,0.376191,0.119597,0.127215,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.00502762,0.0460163,0.048108,0.284593,0.343734,0.306556,0.305777,0.06617,0.503082,0.0391885,0.00488238,0.262537,0.359455,0.226257,0.405955,0.41707,0.00121543,0.0256829,0.753577,0.206222,0.525396,0.651524,0.437176,0.269226,7.22436e-05,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.000185138,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.000155843,0.34988,0.136757,0.00199596,0.0204872,0.262389,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.11631,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.00461664,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.0059529,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.00817962,0.19559,0.132201,0.188694,0.0481795,0.0214786,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.00187586,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.1531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}}
}}

Revision as of 11:49, 5 September 2012


Full id: C4037_Synoviocyte_tenocyte_mesothelioma_left_Olfactory_mesenchymal_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr20:43343476..43343487,+p4@WISP2
Hg19::chr20:43343495..43343509,+p3@WISP2
Hg19::chr20:43343517..43343580,+p2@WISP2


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
fat cell8.80e-0815
Uber Anatomy
Ontology termp-valuen
adult organism9.84e-20115
organism subdivision1.47e-08365
larynx5.73e-089
multi-tissue structure1.42e-07347
surface structure1.43e-0795


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
CEBPB#105137.971147625824820.001974187055288560.0115359548966196
E2F1#186934.907389214879320.008460985347239390.0325856202035672
ESR1#2099330.76860329615453.43136389821584e-050.00067706067289961
FOXA1#3169311.08141974938550.000734755275698670.00582091377066626
FOXA2#3170324.63046375266526.68983856509345e-050.00107324124408571
SMARCB1#6598318.25271578115740.000164397760679890.00203310097426253
TCF7L2#6934310.77017656313730.0008003181298398380.00614500993694625
TFAP2A#7020316.5186343730450.0002218033880766340.00248497361589097
TFAP2C#7022310.80922860986020.0007916746575753130.00616521583494953



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4037&oldid=2130598"