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Coexpression cluster:C4257

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Full id: C4257_Endothelial_basal_Smooth_bone_Renal_mesenchymal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr3:104628747..104628762,-p@chr3:104628747..104628762
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Hg19::chr4:86699902..86699958,+p4@ARHGAP24
Hg19::chr4:86699968..86699983,+p11@ARHGAP24


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
mesodermal cell3.90e-31119
non-terminally differentiated cell6.49e-31180
muscle precursor cell1.54e-2157
myoblast1.54e-2157
multi-potent skeletal muscle stem cell1.54e-2157
muscle cell9.75e-2054
fibroblast3.16e-1975
contractile cell3.64e-1959
endothelial cell of vascular tree1.41e-1824
electrically responsive cell1.16e-1660
electrically active cell1.16e-1660
smooth muscle cell1.08e-1542
smooth muscle myoblast1.08e-1542
vascular associated smooth muscle cell2.20e-1532
blood vessel endothelial cell1.41e-1418
embryonic blood vessel endothelial progenitor cell1.41e-1418
endothelial cell3.12e-1435
meso-epithelial cell3.16e-1244
skin fibroblast3.57e-1123
lining cell4.08e-1057
barrier cell4.08e-1057
embryonic cell2.32e-08248
endothelial cell of artery2.58e-089
cardiocyte9.35e-0816
multi fate stem cell3.31e-07430
Uber Anatomy
Ontology termp-valuen
vessel7.91e-3569
vasculature6.49e-3479
vascular system6.49e-3479
splanchnic layer of lateral plate mesoderm9.92e-3484
blood vessel1.52e-3160
epithelial tube open at both ends1.52e-3160
blood vasculature1.52e-3160
vascular cord1.52e-3160
cardiovascular system1.51e-27110
circulatory system8.02e-27113
somite8.51e-2783
paraxial mesoderm8.51e-2783
presomitic mesoderm8.51e-2783
presumptive segmental plate8.51e-2783
trunk paraxial mesoderm8.51e-2783
presumptive paraxial mesoderm8.51e-2783
dermomyotome1.79e-2570
artery3.56e-2542
arterial blood vessel3.56e-2542
arterial system3.56e-2542
epithelial tube1.13e-23118
multilaminar epithelium7.70e-2282
muscle tissue1.10e-2163
musculature1.10e-2163
musculature of body1.10e-2163
skeletal muscle tissue3.22e-2161
striated muscle tissue3.22e-2161
myotome3.22e-2161
unilaminar epithelium1.42e-20138
systemic artery1.23e-1933
systemic arterial system1.23e-1933
trunk mesenchyme1.20e-18143
endothelium1.41e-1418
blood vessel endothelium1.41e-1418
cardiovascular system endothelium1.41e-1418
trunk9.38e-14216
aorta2.97e-1321
aortic system2.97e-1321
simple squamous epithelium2.57e-1222
cell layer4.82e-12312
epithelium8.56e-12309
squamous epithelium1.02e-1125
anatomical cluster4.50e-11286
anatomical conduit3.58e-10241
mesoderm4.86e-10448
mesoderm-derived structure4.86e-10448
presumptive mesoderm4.86e-10448
integument5.31e-1045
integumental system5.31e-1045
organism subdivision1.06e-09365
multi-cellular organism2.97e-09659
mesenchyme1.42e-08238
entire embryonic mesenchyme1.42e-08238
heart1.63e-0824
primitive heart tube1.63e-0824
primary heart field1.63e-0824
anterior lateral plate mesoderm1.63e-0824
heart tube1.63e-0824
heart primordium1.63e-0824
cardiac mesoderm1.63e-0824
cardiogenic plate1.63e-0824
heart rudiment1.63e-0824
tube2.13e-08194
endothelial tube2.58e-089
arterial system endothelium2.58e-089
endothelium of artery2.58e-089
skin of body2.59e-0840
anatomical system4.15e-08625
anatomical group5.89e-08626
primary circulatory organ1.23e-0727
smooth muscle tissue2.52e-0715
surface structure4.29e-0795


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
BATF#10538216.23853452820240.004917462407809970.023001381960286
BCL11A#53335218.91297006907140.003639406248379680.0183941129101106
FOS#235338.99795530889440.001372499272417130.00899714106904171
IRF4#3662214.60967512449610.006056122473217890.026850712131958



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.