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Coexpression cluster:C1350: Difference between revisions

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|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379997651546202!PRDM1#639;2:43.9436519258203:0.000845206071603017:0.00637254381404472
|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379997651546202!PRDM1#639;2:43.9436519258203:0.000845206071603017:0.00637254381404472
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|tfbs_overrepresentation_for_novel_motifs=1.12961,2.34075,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.800617,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.585619,0.574247,0.396295,0.547818,0.530785,0.92701,0.816912,0.640661,0.35719,0.909936,0.35388,0.585658,0.329602,1.28576,0.355745,0.513952,0.664116,0.390088,0.636689,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,1.50144,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,0.661488,0.987239,1.82799,0.498077,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,1.74379,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,2.24213,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,1.27188,0.306342,1.35665,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.11626
}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1350_neuroectodermal_neuroblastoma_Melanocyte_Smooth_leiomyoma_hepatoma_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:69455914..69455932,+p1@CCND1
Hg19::chr11:69457902..69457918,+p@chr11:69457902..69457918
+
Hg19::chr11:69457929..69457972,+p@chr11:69457929..69457972
+
Hg19::chr11:69458592..69458678,+p4@CCND1
Hg19::chr11:69462821..69462870,+p6@CCND1
Hg19::chr11:69466948..69466985,+p10@CCND1


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>

Uber Anatomy
Ontology termp-valuen
organism subdivision2.17e-23264
trunk5.71e-22199
vessel3.60e-1968
vasculature8.40e-1978
vascular system8.40e-1978
epithelial tube2.36e-18117
artery5.41e-1842
arterial blood vessel5.41e-1842
arterial system5.41e-1842
trunk mesenchyme2.35e-17122
epithelial tube open at both ends2.64e-1759
blood vessel2.64e-1759
blood vasculature2.64e-1759
vascular cord2.64e-1759
unilaminar epithelium3.73e-17148
mesenchyme6.63e-17160
entire embryonic mesenchyme6.63e-17160
epithelial vesicle1.43e-1578
systemic artery2.17e-1533
systemic arterial system2.17e-1533
splanchnic layer of lateral plate mesoderm2.41e-1483
somite2.98e-1471
presomitic mesoderm2.98e-1471
presumptive segmental plate2.98e-1471
dermomyotome2.98e-1471
trunk paraxial mesoderm2.98e-1471
dense mesenchyme tissue4.03e-1473
multilaminar epithelium5.50e-1483
paraxial mesoderm8.76e-1472
presumptive paraxial mesoderm8.76e-1472
multi-cellular organism1.54e-13656
skeletal muscle tissue5.71e-1262
striated muscle tissue5.71e-1262
myotome5.71e-1262
muscle tissue1.62e-1164
musculature1.62e-1164
musculature of body1.62e-1164
surface structure1.83e-1199
cell layer8.89e-11309
epithelium1.12e-10306
cardiovascular system7.63e-10109
circulatory system2.80e-09112
anatomical conduit4.44e-09240
aorta6.24e-0921
aortic system6.24e-0921
anatomical cluster7.64e-09373
subdivision of trunk9.10e-09112
anatomical system9.29e-09624
anatomical group1.54e-08625
multi-tissue structure2.80e-08342
organ component layer4.11e-0866
integument6.44e-0846
integumental system6.44e-0846
blood vessel smooth muscle1.94e-0710
arterial system smooth muscle1.94e-0710
artery smooth muscle tissue1.94e-0710
aorta smooth muscle tissue1.94e-0710
skin of body5.04e-0741


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
POLR2A#543062.147453176558070.01019570676818780.0379997651546202
PRDM1#639243.94365192582030.0008452060716030170.00637254381404472



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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