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Coexpression cluster:C4794

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Full id: C4794_placenta_Smooth_Fibroblast_neuroectodermal_Lens_mesenchymal_chorionic



Phase1 CAGE Peaks

Hg19::chr9:118915849..118915859,+p16@PAPPA
Hg19::chr9:118915863..118915909,+p4@PAPPA
Hg19::chr9:118915915..118915930,+p12@PAPPA


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>


Uber Anatomy
Ontology termp-valuen
somite1.09e-2283
paraxial mesoderm1.09e-2283
presomitic mesoderm1.09e-2283
presumptive segmental plate1.09e-2283
trunk paraxial mesoderm1.09e-2283
presumptive paraxial mesoderm1.09e-2283
dermomyotome9.71e-2270
skeletal muscle tissue7.23e-2161
striated muscle tissue7.23e-2161
myotome7.23e-2161
muscle tissue5.76e-2063
musculature5.76e-2063
musculature of body5.76e-2063
multilaminar epithelium1.66e-1882
trunk mesenchyme2.63e-14143
splanchnic layer of lateral plate mesoderm3.00e-1284
trunk4.19e-11216
organism subdivision6.21e-11365
multi-tissue structure3.26e-09347
heart6.20e-0924
primitive heart tube6.20e-0924
primary heart field6.20e-0924
anterior lateral plate mesoderm6.20e-0924
heart tube6.20e-0924
heart primordium6.20e-0924
cardiac mesoderm6.20e-0924
cardiogenic plate6.20e-0924
heart rudiment6.20e-0924
mesenchyme7.19e-09238
entire embryonic mesenchyme7.19e-09238
artery1.12e-0842
arterial blood vessel1.12e-0842
arterial system1.12e-0842
vasculature1.24e-0879
vascular system1.24e-0879
systemic artery3.27e-0833
systemic arterial system3.27e-0833
primary circulatory organ3.32e-0827
cardiovascular system3.85e-08110
circulatory system5.07e-08113
integument1.59e-0745
integumental system1.59e-0745
unilaminar epithelium3.49e-07138
blood vessel6.53e-0760
epithelial tube open at both ends6.53e-0760
blood vasculature6.53e-0760
vascular cord6.53e-0760
epithelial tube7.47e-07118
skin of body7.53e-0740


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
FOXA1#3169311.08141974938550.000734755275698670.0058475277176479
NR3C1#2908314.9730233311730.0002978331194675480.00310526037377172
REST#597839.650028716128020.001112636247114590.00771956533663726



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.