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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1617_Fibroblast_meningioma_giant_Smooth_mesenchymal_hepatic_Olfactory
|full_id=C1617_Fibroblast_meningioma_giant_Smooth_mesenchymal_hepatic_Olfactory
|id=C1617
|id=C1617

Revision as of 14:12, 12 September 2012


Full id: C1617_Fibroblast_meningioma_giant_Smooth_mesenchymal_hepatic_Olfactory



Phase1 CAGE Peaks

Hg19::chr11:122051194..122051210,-p5@ENST00000533109
Hg19::chr11:122051212..122051237,-p4@ENST00000533109
Hg19::chr11:122051243..122051257,-p3@ENST00000533109
Hg19::chr11:122051315..122051326,-p6@ENST00000533109
Hg19::chr11:122051327..122051348,-p2@ENST00000533109


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
somite6.64e-2483
paraxial mesoderm6.64e-2483
presomitic mesoderm6.64e-2483
presumptive segmental plate6.64e-2483
trunk paraxial mesoderm6.64e-2483
presumptive paraxial mesoderm6.64e-2483
organism subdivision1.13e-19365
multilaminar epithelium2.01e-1982
dermomyotome2.13e-1970
vasculature2.74e-1679
vascular system2.74e-1679
skeletal muscle tissue4.41e-1661
striated muscle tissue4.41e-1661
myotome4.41e-1661
cell layer3.02e-15312
trunk mesenchyme3.29e-15143
muscle tissue3.70e-1563
musculature3.70e-1563
musculature of body3.70e-1563
epithelium2.13e-14309
surface structure4.91e-1495
trunk3.85e-13216
splanchnic layer of lateral plate mesoderm5.02e-1384
artery9.70e-1342
arterial blood vessel9.70e-1342
arterial system9.70e-1342
cardiovascular system3.59e-12110
unilaminar epithelium3.87e-12138
blood vessel4.30e-1260
epithelial tube open at both ends4.30e-1260
blood vasculature4.30e-1260
vascular cord4.30e-1260
vessel5.67e-1269
multi-tissue structure7.69e-12347
circulatory system3.15e-11113
systemic artery7.22e-1133
systemic arterial system7.22e-1133
skin of body7.20e-1040
integument7.23e-1045
integumental system7.23e-1045
epithelial tube3.89e-09118
anatomical cluster5.22e-09286
mesenchyme7.36e-08238
entire embryonic mesenchyme7.36e-08238
aorta7.41e-0821
aortic system7.41e-0821
multi-cellular organism3.10e-07659
anatomical conduit3.20e-07241
anatomical system7.40e-07625


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#105157.971147625824823.10621793420244e-050.000628215133288475
EP300#203356.77394172622327.00901578206049e-050.00110676534512037
FOS#235358.99795530889441.69470025615156e-050.000388568166964243
GATA2#2624512.7449317335542.9719152914525e-060.000101003534371626
NR3C1#2908514.9730233311731.32777388277837e-065.23683446161216e-05
STAT3#6774510.51946499715427.759040745861e-060.000220143019955712
TCF7L2#6934510.77017656313736.89693748574565e-060.00019947639270944



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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