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Coexpression cluster:C4562: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.15e-17!115;UBERON:0000481!7.85e-13!347;UBERON:0000073!3.37e-11!94;UBERON:0001016!3.37e-11!94;UBERON:0001049!1.16e-10!57;UBERON:0005068!1.16e-10!57;UBERON:0006241!1.16e-10!57;UBERON:0007135!1.16e-10!57;UBERON:0003075!1.45e-10!86;UBERON:0007284!1.45e-10!86;UBERON:0000153!1.87e-10!129;UBERON:0007811!1.87e-10!129;UBERON:0002346!4.81e-10!90;UBERON:0000475!7.93e-10!365;UBERON:0000033!8.22e-10!123;UBERON:0000922!1.04e-09!612;UBERON:0002050!1.15e-09!605;UBERON:0005423!1.15e-09!605;UBERON:0000923!2.03e-09!604;UBERON:0005291!2.03e-09!604;UBERON:0006598!2.03e-09!604;UBERON:0002532!2.03e-09!604;UBERON:0005743!2.33e-09!86;UBERON:0002616!2.45e-09!59;UBERON:0001017!3.85e-09!82;UBERON:0000955!4.75e-09!69;UBERON:0006238!4.75e-09!69;UBERON:0004121!1.15e-08!169;UBERON:0000924!2.00e-08!173;UBERON:0006601!2.00e-08!173;UBERON:0003080!4.07e-08!42;UBERON:0002780!8.02e-08!41;UBERON:0001890!8.02e-08!41;UBERON:0006240!8.02e-08!41;UBERON:0003056!1.12e-07!61;UBERON:0000468!4.70e-07!659
|ontology_enrichment_uberon=UBERON:0007023!3.15e-17!115;UBERON:0000481!7.85e-13!347;UBERON:0000073!3.37e-11!94;UBERON:0001016!3.37e-11!94;UBERON:0001049!1.16e-10!57;UBERON:0005068!1.16e-10!57;UBERON:0006241!1.16e-10!57;UBERON:0007135!1.16e-10!57;UBERON:0003075!1.45e-10!86;UBERON:0007284!1.45e-10!86;UBERON:0000153!1.87e-10!129;UBERON:0007811!1.87e-10!129;UBERON:0002346!4.81e-10!90;UBERON:0000475!7.93e-10!365;UBERON:0000033!8.22e-10!123;UBERON:0000922!1.04e-09!612;UBERON:0002050!1.15e-09!605;UBERON:0005423!1.15e-09!605;UBERON:0000923!2.03e-09!604;UBERON:0005291!2.03e-09!604;UBERON:0006598!2.03e-09!604;UBERON:0002532!2.03e-09!604;UBERON:0005743!2.33e-09!86;UBERON:0002616!2.45e-09!59;UBERON:0001017!3.85e-09!82;UBERON:0000955!4.75e-09!69;UBERON:0006238!4.75e-09!69;UBERON:0004121!1.15e-08!169;UBERON:0000924!2.00e-08!173;UBERON:0006601!2.00e-08!173;UBERON:0003080!4.07e-08!42;UBERON:0002780!8.02e-08!41;UBERON:0001890!8.02e-08!41;UBERON:0006240!8.02e-08!41;UBERON:0003056!1.12e-07!61;UBERON:0000468!4.70e-07!659
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281054121632153!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00722798302145405!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618365937944119
|tfbs_overrepresentation=0.147255,0.0586687,0.00948065,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.00920475,0.081977,0.00465244,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.000210711,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.0244227,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0124566,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.0259741,0.0409286,0.0669887,0.0649715,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.00428542,0.114283,0.0400322,0.00847953,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.0103428,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.00976435,0.00360981,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.0800546,0.15606,0.161026,0.0738599,0.000373694,0.000497929,0.085973,0.060453,0.059896,0.569726,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.0177645,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.0183114,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0121776,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.0356268,0.446759,0.0865903,0.0380459,0.130174,0.000303948,0.0381789,0.0199061,0.0821962,0.20128,0.0986134,0.00690237,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.147559,0.330703,0.395854,0.061507,0.53472,0.0724671,0.000328487,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.0821552,0.463191,0.0883629,0.173877,0.03861,0.0792797,0.0173702,0.142924,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.0340949,0.0146955,0.0447111,0.314747,0.577664,0.291709,0.120054,0.576651,0.416816,0.292835,0.137839,0.439556,0.373868,0.213592,0.0694028,0.18237,0.0359955,0.00847576,1.43819e-05,0.275351,0.236471,0.185661,0.346319,0.00117453,0.270984,0.258117,0.503058,0.163222,0.0389686,0.248634,0.0439966,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.176034,0.217247,0.412837,0.671377,0.188159,0.0477082,0.120021,0.218623,0.0550136,0.00142673,0.0451077,0.0747529,0.229003,0.28275,0.0129683,0.50215,0.294698,0.34331,0.0282052,0.289204,0.0605279,0.000194033,0.278044,0.0015747,0.428671,0.228096,0.0642385,0.19763,0.15631,0.0106166,0.421464,0.48267,0.420626,0.165111,0.0150702,0.335105,0.144809,0.0005766,0.08628,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.0526965,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.130283,0.0538047,0.206222,0.00713629,0.0905337,0.437176,0.040018,0.339277,0.552319,0.281425,0.0105593,0.0238793,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.00103044,0.0769581,0.347298,0.182325,0.0699395,0.475069,0.0958562,0.6408,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.00601662,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0842821,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.00683084,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.0238665,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.062811,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.00594521,0.0419304,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.15318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}}
}}

Revision as of 13:08, 5 September 2012


Full id: C4562_skeletal_leiomyoblastoma_migratory_pineal_merkel_rhabdomyosarcoma_gall



Phase1 CAGE Peaks

Hg19::chr6:133562472..133562530,+p1@EYA4
Hg19::chr6:133562704..133562733,+p3@EYA4
Hg19::chr6:133562744..133562760,+p4@EYA4


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.15e-17115
multi-tissue structure7.85e-13347
regional part of nervous system3.37e-1194
nervous system3.37e-1194
neural tube1.16e-1057
neural rod1.16e-1057
future spinal cord1.16e-1057
neural keel1.16e-1057
neural plate1.45e-1086
presumptive neural plate1.45e-1086
anterior region of body1.87e-10129
craniocervical region1.87e-10129
neurectoderm4.81e-1090
organism subdivision7.93e-10365
head8.22e-10123
embryo1.04e-09612
embryonic structure1.15e-09605
developing anatomical structure1.15e-09605
germ layer2.03e-09604
embryonic tissue2.03e-09604
presumptive structure2.03e-09604
epiblast (generic)2.03e-09604
regional part of brain2.45e-0959
central nervous system3.85e-0982
brain4.75e-0969
future brain4.75e-0969
ectoderm-derived structure1.15e-08169
ectoderm2.00e-08173
presumptive ectoderm2.00e-08173
anterior neural tube4.07e-0842
regional part of forebrain8.02e-0841
forebrain8.02e-0841
future forebrain8.02e-0841
pre-chordal neural plate1.12e-0761
multi-cellular organism4.70e-07659


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
CTCF#1066435.360256373075030.0064925092527670.0281054121632153
MXI1#460139.96157162875930.001011470541259020.00722798302145405
TFAP2C#7022310.80922860986020.0007916746575753130.00618365937944119



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:C4562&oldid=2131933"