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Coexpression cluster:C3622: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3622_Mesenchymal_Alveolar_Renal_Smooth_Osteoblast_Keratocytes_Hair
|full_id=C3622_Mesenchymal_Alveolar_Renal_Smooth_Osteoblast_Keratocytes_Hair
|id=C3622
|id=C3622

Revision as of 16:34, 12 September 2012


Full id: C3622_Mesenchymal_Alveolar_Renal_Smooth_Osteoblast_Keratocytes_Hair



Phase1 CAGE Peaks

Hg19::chr17:27044810..27044873,-p2@RAB34
Hg19::chr17:27044878..27044894,-p3@RAB34
Hg19::chr17:27045165..27045230,-p1@RAB34


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
somite4.34e-2483
paraxial mesoderm4.34e-2483
presomitic mesoderm4.34e-2483
presumptive segmental plate4.34e-2483
trunk paraxial mesoderm4.34e-2483
presumptive paraxial mesoderm4.34e-2483
multilaminar epithelium3.24e-2382
dermomyotome1.62e-2170
trunk mesenchyme8.05e-21143
trunk4.55e-18216
mesenchyme1.14e-17238
entire embryonic mesenchyme1.14e-17238
skeletal muscle tissue1.46e-1761
striated muscle tissue1.46e-1761
myotome1.46e-1761
muscle tissue8.16e-1763
musculature8.16e-1763
musculature of body8.16e-1763
multi-tissue structure3.18e-14347
organism subdivision2.38e-13365
multi-cellular organism3.82e-11659
surface structure4.71e-1195
splanchnic layer of lateral plate mesoderm2.01e-1084
epithelial tube3.06e-10118
mesoderm3.31e-10448
mesoderm-derived structure3.31e-10448
presumptive mesoderm3.31e-10448
artery1.01e-0942
arterial blood vessel1.01e-0942
arterial system1.01e-0942
embryo3.03e-09612
embryonic structure4.83e-09605
developing anatomical structure4.83e-09605
cell layer4.93e-09312
germ layer5.53e-09604
embryonic tissue5.53e-09604
presumptive structure5.53e-09604
epiblast (generic)5.53e-09604
vasculature6.05e-0979
vascular system6.05e-0979
anatomical system8.27e-09625
epithelium8.81e-09309
anatomical group1.59e-08626
unilaminar epithelium2.94e-08138
blood vessel5.05e-0860
epithelial tube open at both ends5.05e-0860
blood vasculature5.05e-0860
vascular cord5.05e-0860
integument5.07e-0845
integumental system5.07e-0845
systemic artery5.35e-0833
systemic arterial system5.35e-0833
compound organ8.43e-0869
skin of body5.53e-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
FOS#235338.99795530889440.001372499272417130.00896674912498264
JUND#372736.994663941871030.002921845042734990.0156561784627879
SMARCB1#6598212.16847718743830.008675002221921740.0329817457974257
SMARCC1#6599343.66335931963151.20046018043203e-050.000301599376435268
SMARCC2#6601394.15537442689761.19621075407887e-064.85169145418419e-05
STAT3#6774310.51946499715420.0008589184530415310.00642352913119975



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.

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