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Coexpression cluster:C2729: Difference between revisions

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|tf_chipseq_enrich=TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244745100923969!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249507619860347
|tf_chipseq_enrich=TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244745100923969!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249507619860347
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}}
}}

Revision as of 15:41, 26 November 2012


Full id: C2729_small_colon_mature_Hair_Adipocyte_temporal_duodenum



Phase1 CAGE Peaks

Hg19::chr3:154797877..154797889,+p12@MME
Hg19::chr3:154797911..154797914,+p19@MME
Hg19::chr3:154797928..154797939,+p18@MME
Hg19::chr3:154797941..154797948,+p20@MME


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>


Cell Type
Ontology termp-valuen
fibroblast1.81e-1176
fat cell2.64e-0915
skin fibroblast4.39e-0923
cell of skeletal muscle1.13e-079
multi fate stem cell1.21e-07427
muscle precursor cell2.29e-0758
myoblast2.29e-0758
multi-potent skeletal muscle stem cell2.29e-0758
somatic stem cell2.70e-07433
Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue2.45e-0973
mesenchyme3.46e-09160
entire embryonic mesenchyme3.46e-09160
somite3.56e-0971
presomitic mesoderm3.56e-0971
presumptive segmental plate3.56e-0971
dermomyotome3.56e-0971
trunk paraxial mesoderm3.56e-0971
paraxial mesoderm7.01e-0972
presumptive paraxial mesoderm7.01e-0972
integument8.61e-0946
integumental system8.61e-0946
trunk9.58e-09199
trunk mesenchyme1.49e-08122
muscle tissue9.58e-0864
musculature9.58e-0864
musculature of body9.58e-0864
surface structure1.27e-0799
skeletal muscle tissue1.84e-0762
striated muscle tissue1.84e-0762
myotome1.84e-0762
organism subdivision1.84e-07264
epithelial vesicle2.58e-0778
multilaminar epithelium4.74e-0783
skin of body4.91e-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)

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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
TBP#690843.706770687096390.005296377814784350.0244745100923969
ZNF263#1012748.221841637010680.0002187871180958320.00249507619860347



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.