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Coexpression cluster:C2728

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Full id: C2728_Smooth_Neutrophils_Pancreatic_tridermal_Fibroblast_mesenchymal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr3:154797636..154797696,+p1@MME
Hg19::chr3:154797700..154797725,+p4@MME
Hg19::chr3:154797727..154797746,+p7@MME
Hg19::chr3:154797781..154797800,+p6@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
fibroblast1.00e-1976
muscle precursor cell9.51e-1658
myoblast9.51e-1658
multi-potent skeletal muscle stem cell9.51e-1658
non-terminally differentiated cell2.35e-14106
muscle cell2.77e-1455
contractile cell8.78e-1259
electrically responsive cell1.04e-1161
electrically active cell1.04e-1161
skin fibroblast2.76e-1123
smooth muscle cell2.51e-1043
smooth muscle myoblast2.51e-1043
multi fate stem cell1.12e-09427
somatic stem cell7.20e-09433
stem cell1.35e-08441
somatic cell3.76e-08588
fat cell4.32e-0715
Uber Anatomy
Ontology termp-valuen
somite1.12e-1971
presomitic mesoderm1.12e-1971
presumptive segmental plate1.12e-1971
dermomyotome1.12e-1971
trunk paraxial mesoderm1.12e-1971
dense mesenchyme tissue2.40e-1973
paraxial mesoderm6.95e-1972
presumptive paraxial mesoderm6.95e-1972
multilaminar epithelium1.45e-1683
epithelial vesicle8.26e-1678
skeletal muscle tissue1.75e-1562
striated muscle tissue1.75e-1562
myotome1.75e-1562
muscle tissue4.26e-1564
musculature4.26e-1564
musculature of body4.26e-1564
surface structure5.34e-1499
trunk mesenchyme7.75e-12122
mesenchyme1.39e-11160
entire embryonic mesenchyme1.39e-11160
organism subdivision2.01e-11264
integument1.10e-1046
integumental system1.10e-1046
unilaminar epithelium2.23e-10148
skin of body8.72e-0941
trunk1.51e-08199
organ component layer6.07e-0766


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
CTCF#1066445.360256373075030.001211145381643620.00818710760605038
ZNF263#1012748.221841637010680.0002187871180958320.00249480378063223



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.