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Coexpression cluster:C807: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C807_neuroectodermal_renal_leiomyoma_Smooth_neuroblastoma_Aortic_Melanocyte
|full_id=C807_neuroectodermal_renal_leiomyoma_Smooth_neuroblastoma_Aortic_Melanocyte
|id=C807
|id=C807

Revision as of 18:32, 12 September 2012


Full id: C807_neuroectodermal_renal_leiomyoma_Smooth_neuroblastoma_Aortic_Melanocyte



Phase1 CAGE Peaks

Hg19::chr11:69466307..69466329,+p@chr11:69466307..69466329
+
Hg19::chr11:69466430..69466446,+p@chr11:69466430..69466446
+
Hg19::chr11:69466577..69466634,+p@chr11:69466577..69466634
+
Hg19::chr11:69467214..69467238,+p5@CCND1
Hg19::chr11:69467344..69467411,+p2@CCND1
Hg19::chr11:69467416..69467438,+p7@CCND1
Hg19::chr11:69467457..69467532,+p3@CCND1
Hg19::chr11:69467977..69467992,+p@chr11:69467977..69467992
+
Hg19::chr11:69468195..69468212,+p@chr11:69468195..69468212
+
Hg19::chr11:69468466..69468480,+p@chr11:69468466..69468480
+


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>


Uber Anatomy
Ontology termp-valuen
trunk7.05e-21216
trunk mesenchyme1.07e-18143
organism subdivision7.47e-17365
epithelial tube2.27e-16118
vasculature8.45e-1579
vascular system8.45e-1579
multi-cellular organism1.10e-14659
vessel4.31e-1469
artery6.93e-1442
arterial blood vessel6.93e-1442
arterial system6.93e-1442
mesenchyme1.39e-13238
entire embryonic mesenchyme1.39e-13238
blood vessel1.55e-1360
epithelial tube open at both ends1.55e-1360
blood vasculature1.55e-1360
vascular cord1.55e-1360
unilaminar epithelium1.83e-13138
multilaminar epithelium4.56e-1382
somite6.62e-1383
paraxial mesoderm6.62e-1383
presomitic mesoderm6.62e-1383
presumptive segmental plate6.62e-1383
trunk paraxial mesoderm6.62e-1383
presumptive paraxial mesoderm6.62e-1383
dermomyotome7.56e-1270
systemic artery8.93e-1233
systemic arterial system8.93e-1233
splanchnic layer of lateral plate mesoderm9.25e-1284
epithelium2.37e-11309
cell layer2.74e-11312
multi-tissue structure5.13e-11347
skeletal muscle tissue9.41e-1161
striated muscle tissue9.41e-1161
myotome9.41e-1161
muscle tissue3.28e-1063
musculature3.28e-1063
musculature of body3.28e-1063
surface structure5.16e-1095
anatomical system5.47e-10625
anatomical group1.00e-09626
anatomical cluster2.25e-08286
anatomical conduit3.45e-08241
subdivision of trunk5.63e-08113
organ component layer1.35e-0757
cardiovascular system1.52e-07110
circulatory system2.39e-07113
aorta3.15e-0721
aortic system3.15e-0721
integument5.22e-0745
integumental system5.22e-0745
embryo6.37e-07612
embryonic structure9.17e-07605
developing anatomical structure9.17e-07605
germ layer9.83e-07604
embryonic tissue9.83e-07604
presumptive structure9.83e-07604
epiblast (generic)9.83e-07604
Disease
Ontology termp-valuen
cell type cancer1.39e-07143


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


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.