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Coexpression cluster:C4674: Difference between revisions

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|ontology_enrichment_disease=DOID:305!7.32e-13!106;DOID:0050687!1.52e-08!143
|ontology_enrichment_disease=DOID:305!7.32e-13!106;DOID:0050687!1.52e-08!143
|ontology_enrichment_uberon=UBERON:0007023!8.12e-27!115;UBERON:0001049!1.16e-20!57;UBERON:0005068!1.16e-20!57;UBERON:0006241!1.16e-20!57;UBERON:0007135!1.16e-20!57;UBERON:0003080!1.53e-20!42;UBERON:0002780!4.51e-20!41;UBERON:0001890!4.51e-20!41;UBERON:0006240!4.51e-20!41;UBERON:0000955!1.65e-19!69;UBERON:0006238!1.65e-19!69;UBERON:0001017!2.47e-19!82;UBERON:0005743!1.17e-18!86;UBERON:0001869!1.88e-18!32;UBERON:0000073!2.15e-18!94;UBERON:0001016!2.15e-18!94;UBERON:0002616!6.12e-18!59;UBERON:0001893!9.72e-18!34;UBERON:0002791!4.49e-17!33;UBERON:0002020!4.99e-17!34;UBERON:0003528!4.99e-17!34;UBERON:0000153!1.57e-15!129;UBERON:0007811!1.57e-15!129;UBERON:0003056!3.40e-15!61;UBERON:0002619!3.83e-15!22;UBERON:0003075!5.20e-15!86;UBERON:0007284!5.20e-15!86;UBERON:0000033!7.46e-15!123;UBERON:0000956!3.10e-14!25;UBERON:0000203!3.10e-14!25;UBERON:0004111!4.34e-14!241;UBERON:0001950!4.78e-14!20;UBERON:0002346!9.29e-14!90;UBERON:0004121!9.84e-14!169;UBERON:0000924!5.48e-13!173;UBERON:0006601!5.48e-13!173;UBERON:0000025!2.32e-11!194;UBERON:0000477!8.19e-10!286;UBERON:0000064!3.77e-09!219;UBERON:0001007!8.22e-09!155;UBERON:0001555!8.22e-09!155;UBERON:0007026!8.22e-09!155;UBERON:0004921!1.15e-08!129;UBERON:0004185!1.15e-08!129;UBERON:0004119!1.57e-08!169;UBERON:0000925!1.57e-08!169;UBERON:0006595!1.57e-08!169;UBERON:0000483!1.31e-07!309;UBERON:0000481!1.48e-07!347;UBERON:0000119!2.36e-07!312;UBERON:0005911!8.63e-07!82
|ontology_enrichment_uberon=UBERON:0007023!8.12e-27!115;UBERON:0001049!1.16e-20!57;UBERON:0005068!1.16e-20!57;UBERON:0006241!1.16e-20!57;UBERON:0007135!1.16e-20!57;UBERON:0003080!1.53e-20!42;UBERON:0002780!4.51e-20!41;UBERON:0001890!4.51e-20!41;UBERON:0006240!4.51e-20!41;UBERON:0000955!1.65e-19!69;UBERON:0006238!1.65e-19!69;UBERON:0001017!2.47e-19!82;UBERON:0005743!1.17e-18!86;UBERON:0001869!1.88e-18!32;UBERON:0000073!2.15e-18!94;UBERON:0001016!2.15e-18!94;UBERON:0002616!6.12e-18!59;UBERON:0001893!9.72e-18!34;UBERON:0002791!4.49e-17!33;UBERON:0002020!4.99e-17!34;UBERON:0003528!4.99e-17!34;UBERON:0000153!1.57e-15!129;UBERON:0007811!1.57e-15!129;UBERON:0003056!3.40e-15!61;UBERON:0002619!3.83e-15!22;UBERON:0003075!5.20e-15!86;UBERON:0007284!5.20e-15!86;UBERON:0000033!7.46e-15!123;UBERON:0000956!3.10e-14!25;UBERON:0000203!3.10e-14!25;UBERON:0004111!4.34e-14!241;UBERON:0001950!4.78e-14!20;UBERON:0002346!9.29e-14!90;UBERON:0004121!9.84e-14!169;UBERON:0000924!5.48e-13!173;UBERON:0006601!5.48e-13!173;UBERON:0000025!2.32e-11!194;UBERON:0000477!8.19e-10!286;UBERON:0000064!3.77e-09!219;UBERON:0001007!8.22e-09!155;UBERON:0001555!8.22e-09!155;UBERON:0007026!8.22e-09!155;UBERON:0004921!1.15e-08!129;UBERON:0004185!1.15e-08!129;UBERON:0004119!1.57e-08!169;UBERON:0000925!1.57e-08!169;UBERON:0006595!1.57e-08!169;UBERON:0000483!1.31e-07!309;UBERON:0000481!1.48e-07!347;UBERON:0000119!2.36e-07!312;UBERON:0005911!8.63e-07!82
|tfbs_overrepresentation=0.147255,0.0586687,0.00192761,0.0477154,0.199763,0.287811,0.0430074,0.000235346,0.03272,0.0257057,0.139423,0.0275521,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.00424558,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,1.85009e-13,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.00190755,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.00183766,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,5.63916e-05,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.0415725,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.00181106,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.0223702,0.155998,0.00243119,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.0174119,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.0281563,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.00111717,0.00995227,0.46397,0.0541353,0.00328329,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0108418,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,6.0212e-06,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0119747,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.00029312,0.0619218,0.0163125,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.254773,3.60802e-05,0.0865903,0.0380459,0.130174,0.059488,0.00909613,0.00102762,0.268011,0.563047,0.0319444,1.82637e-07,0.0638737,0.0790073,0.261553,0.446302,0.373681,0.309233,0.147559,0.330703,0.0146881,0.061507,0.0078057,0.248224,0.271958,0.292154,0.0159894,0.39729,0.581713,0.597171,0.187251,0.0756284,0.181715,0.0186051,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.173877,0.168255,0.370782,0.101703,0.484505,0.253571,0.276829,0.0509673,0.481778,0.316882,0.223503,0.0340949,0.236436,0.283727,0.0557438,0.577664,0.291709,0.448095,0.0563639,0.0175396,0.292835,0.476744,0.439556,0.373868,0.0116572,0.241757,0.18237,0.126021,3.81541e-08,9.55652e-05,0.275351,0.0304678,0.185661,0.346319,0.179399,0.270984,0.258117,0.503058,0.513852,0.000119998,0.248634,0.281576,0.000524881,0.0141151,0.0670502,0.0730934,0.184794,0.596648,0.0582356,0.0583074,0.412837,0.671377,0.188159,0.191921,0.00324632,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.000323853,0.50215,0.294698,0.34331,0.477304,0.00514398,0.327108,0.0295492,0.278044,0.0015747,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.0293525,0.420626,0.0374607,1.62855e-07,0.335105,0.144809,0.145539,0.08628,0.0123475,0.0224279,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.00541072,0.284593,0.00911104,0.306556,0.305777,0.601433,0.503082,0.169823,0.284629,0.262537,0.010587,0.226257,0.0965765,2.1658e-05,0.363685,0.000474832,1.63525e-05,0.206222,0.525396,0.0905337,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.00680512,0.159617,0.238587,0.000124053,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.347298,0.539392,0.34988,0.475069,0.0958562,0.6408,0.0186811,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,2.73054e-06,0.191777,0.111931,0.28934,0.0435386,0.0515253,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.0517437,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.000107423,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.00146083,0.132201,1.74564e-12,0.0481795,0.0214786,1.19156e-11,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.0268081,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.13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}}
}}

Revision as of 20:13, 8 August 2012


Full id: C4674_lymphoma_diffuse_small_smallcell_caudate_acute_signet



Phase1 CAGE Peaks

Hg19::chr7:22396727..22396787,-p2@RAPGEF5
Hg19::chr7:22396791..22396818,-p9@RAPGEF5
Hg19::chr7:22396829..22396835,-p14@RAPGEF5


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
epithelial cell1.46e-11254
endodermal cell2.95e-0759
lymphocyte of B lineage4.53e-0724
pro-B cell4.53e-0724
Uber Anatomy
Ontology termp-valuen
adult organism8.12e-27115
neural tube1.16e-2057
neural rod1.16e-2057
future spinal cord1.16e-2057
neural keel1.16e-2057
anterior neural tube1.53e-2042
regional part of forebrain4.51e-2041
forebrain4.51e-2041
future forebrain4.51e-2041
brain1.65e-1969
future brain1.65e-1969
central nervous system2.47e-1982
cerebral hemisphere1.88e-1832
regional part of nervous system2.15e-1894
nervous system2.15e-1894
regional part of brain6.12e-1859
telencephalon9.72e-1834
regional part of telencephalon4.49e-1733
gray matter4.99e-1734
brain grey matter4.99e-1734
anterior region of body1.57e-15129
craniocervical region1.57e-15129
pre-chordal neural plate3.40e-1561
regional part of cerebral cortex3.83e-1522
neural plate5.20e-1586
presumptive neural plate5.20e-1586
head7.46e-15123
cerebral cortex3.10e-1425
pallium3.10e-1425
anatomical conduit4.34e-14241
neocortex4.78e-1420
neurectoderm9.29e-1490
ectoderm-derived structure9.84e-14169
ectoderm5.48e-13173
presumptive ectoderm5.48e-13173
tube2.32e-11194
anatomical cluster8.19e-10286
organ part3.77e-09219
digestive system8.22e-09155
digestive tract8.22e-09155
primitive gut8.22e-09155
subdivision of digestive tract1.15e-08129
endodermal part of digestive tract1.15e-08129
endoderm-derived structure1.57e-08169
endoderm1.57e-08169
presumptive endoderm1.57e-08169
epithelium1.31e-07309
multi-tissue structure1.48e-07347
cell layer2.36e-07312
endo-epithelium8.63e-0782
Disease
Ontology termp-valuen
carcinoma7.32e-13106
cell type cancer1.52e-08143


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)

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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

No analysis results for this cluster

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.

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