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Coexpression cluster:C3970

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Full id: C3970_Smooth_Fibroblast_basal_Mesothelial_mesenchymal_leiomyoma_Aortic



Phase1 CAGE Peaks

Hg19::chr1:32264166..32264245,-p2@SPOCD1
Hg19::chr1:32264250..32264354,-p1@SPOCD1
Hg19::chr1:32264356..32264380,-p3@SPOCD1


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
somite1.41e-2483
paraxial mesoderm1.41e-2483
presomitic mesoderm1.41e-2483
presumptive segmental plate1.41e-2483
trunk paraxial mesoderm1.41e-2483
presumptive paraxial mesoderm1.41e-2483
vasculature2.40e-2479
vascular system2.40e-2479
dermomyotome8.32e-2370
multilaminar epithelium1.03e-2282
cardiovascular system2.32e-22110
artery2.34e-2242
arterial blood vessel2.34e-2242
arterial system2.34e-2242
vessel4.69e-2269
blood vessel5.09e-2160
epithelial tube open at both ends5.09e-2160
blood vasculature5.09e-2160
vascular cord5.09e-2160
circulatory system9.55e-21113
skeletal muscle tissue6.67e-2061
striated muscle tissue6.67e-2061
myotome6.67e-2061
splanchnic layer of lateral plate mesoderm8.70e-2084
trunk mesenchyme1.68e-19143
muscle tissue3.12e-1963
musculature3.12e-1963
musculature of body3.12e-1963
epithelial tube4.77e-18118
systemic artery1.17e-1733
systemic arterial system1.17e-1733
unilaminar epithelium2.84e-17138
trunk4.41e-14216
organism subdivision6.63e-14365
cell layer1.45e-13312
epithelium5.23e-13309
aorta3.95e-1021
aortic system3.95e-1021
anatomical system4.30e-09625
anatomical group6.90e-09626
multi-cellular organism7.66e-09659
surface structure1.04e-0895
integument3.39e-0845
integumental system3.39e-0845
anatomical conduit8.58e-08241
blood vessel smooth muscle2.08e-0710
arterial system smooth muscle2.08e-0710
artery smooth muscle tissue2.08e-0710
aorta smooth muscle tissue2.08e-0710
simple squamous epithelium2.34e-0722
anatomical cluster3.73e-07286
multi-tissue structure3.79e-07347
tube6.50e-07194
mesenchyme6.97e-07238
entire embryonic mesenchyme6.97e-07238
skin of body7.76e-0740
endothelium9.40e-0718
blood vessel endothelium9.40e-0718
cardiovascular system endothelium9.40e-0718
Disease
Ontology termp-valuen
ovarian cancer1.28e-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)

{{{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
CEBPB#105137.971147625824820.001974187055288560.0115288594200001
EGR1#195834.988179094810140.008056488137383440.0320928966580284
FOS#235338.99795530889440.001372499272417130.00898248223536612
FOSL1#8061339.7135797163731.59554825631833e-050.000371378347095231
JUN#3725312.51282919233630.0005103313992726250.00444561689954406
JUNB#3726330.61063265982113.4847716247536e-050.000680909380201387
JUND#372736.994663941871030.002921845042734990.0156916015024528
SMARCC1#6599343.66335931963151.20046018043203e-050.000301962574142921



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.