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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 17:38, 8 August 2012


Full id: C1779_Osteoblast_Fibroblast_Mesenchymal_Smooth_normal_Pericytes_Nucleus



Phase1 CAGE Peaks

Hg19::chr17:39975772..39975795,+p6@FKBP10
Hg19::chr7:100201692..100201773,+p8@PCOLCE
Hg19::chr7:100202771..100202805,+p7@PCOLCE
Hg19::chr7:100204173..100204212,+p10@PCOLCE
Hg19::chr7:100205345..100205374,+p@chr7:100205345..100205374
+


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


GO IDGO nameFDR corrected p-value
GO:0005518collagen binding0.0391395160907413
GO:0005788endoplasmic reticulum lumen0.0478422291454966
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0478422291454966
GO:0016859cis-trans isomerase activity0.0478422291454966



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
somite3.77e-2183
paraxial mesoderm3.77e-2183
presomitic mesoderm3.77e-2183
presumptive segmental plate3.77e-2183
trunk paraxial mesoderm3.77e-2183
presumptive paraxial mesoderm3.77e-2183
dermomyotome9.78e-2070
skeletal muscle tissue2.97e-1761
striated muscle tissue2.97e-1761
myotome2.97e-1761
muscle tissue5.24e-1763
musculature5.24e-1763
musculature of body5.24e-1763
trunk mesenchyme5.33e-17143
multilaminar epithelium1.40e-1682
trunk9.25e-13216
organism subdivision8.32e-12365
splanchnic layer of lateral plate mesoderm9.10e-1184
integument1.82e-1045
integumental system1.82e-1045
surface structure3.13e-1095
unilaminar epithelium9.56e-10138
mesenchyme7.14e-09238
entire embryonic mesenchyme7.14e-09238
artery1.57e-0842
arterial blood vessel1.57e-0842
arterial system1.57e-0842
vasculature3.12e-0879
vascular system3.12e-0879
epithelial tube3.26e-08118
skin of body4.54e-0840
multi-cellular organism8.90e-08659
systemic artery1.03e-0733
systemic arterial system1.03e-0733
blood vessel1.04e-0760
epithelial tube open at both ends1.04e-0760
blood vasculature1.04e-0760
vascular cord1.04e-0760
multi-tissue structure1.15e-07347
cell layer4.13e-07312
adipose tissue4.70e-0714
epithelium9.00e-07309


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.