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Coexpression cluster:C1080: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1080_Fibroblast_mesenchymal_neuroectodermal_Hair_Mesenchymal_Smooth_alveolar
|full_id=C1080_Fibroblast_mesenchymal_neuroectodermal_Hair_Mesenchymal_Smooth_alveolar
|id=C1080
|id=C1080

Revision as of 13:31, 12 September 2012


Full id: C1080_Fibroblast_mesenchymal_neuroectodermal_Hair_Mesenchymal_Smooth_alveolar



Phase1 CAGE Peaks

Hg19::chr3:55521323..55521342,-p5@WNT5A
Hg19::chr3:55521350..55521362,-p17@WNT5A
Hg19::chr3:55521543..55521588,-p7@WNT5A
Hg19::chr3:55521611..55521652,-p8@WNT5A
Hg19::chr3:55521660..55521688,-p11@WNT5A
Hg19::chr3:55522284..55522331,-p@chr3:55522284..55522331
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Hg19::chr3:55522429..55522447,-p@chr3:55522429..55522447
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Hg19::chr3:55522502..55522553,-p@chr3:55522502..55522553
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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 subdivision2.93e-14365
multi-cellular organism7.92e-14659
somite8.01e-1283
paraxial mesoderm8.01e-1283
presomitic mesoderm8.01e-1283
presumptive segmental plate8.01e-1283
trunk paraxial mesoderm8.01e-1283
presumptive paraxial mesoderm8.01e-1283
surface structure2.05e-1195
anatomical system1.13e-10625
anatomical group1.44e-10626
multi-tissue structure1.60e-10347
multilaminar epithelium6.69e-1082
dermomyotome3.06e-0970
embryo1.67e-08612
embryonic structure3.01e-08605
developing anatomical structure3.01e-08605
skeletal muscle tissue4.13e-0861
striated muscle tissue4.13e-0861
myotome4.13e-0861
germ layer4.87e-08604
embryonic tissue4.87e-08604
presumptive structure4.87e-08604
epiblast (generic)4.87e-08604
trunk mesenchyme5.76e-08143
extraembryonic structure6.02e-0824
organ6.90e-08511
muscle tissue7.62e-0863
musculature7.62e-0863
musculature of body7.62e-0863
integument9.78e-0845
integumental system9.78e-0845
mesenchyme2.81e-07238
entire embryonic mesenchyme2.81e-07238
extraembryonic membrane5.69e-0714
membranous layer5.69e-0714


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066485.360256373075031.46631949289063e-065.66559162108785e-05
GTF2F1#296257.962288047973530.0001362053831339150.0017808154743519
POLR2A#543082.147453176558070.002210725788971910.012723094212511
TBP#690883.706770687096392.80450451364125e-050.000592194999798176



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.