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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2652_acute_Hepatic_Endothelial_Renal_heart_breast_spleen
|full_id=C2652_acute_Hepatic_Endothelial_Renal_heart_breast_spleen
|id=C2652
|id=C2652

Revision as of 15:25, 12 September 2012


Full id: C2652_acute_Hepatic_Endothelial_Renal_heart_breast_spleen



Phase1 CAGE Peaks

Hg19::chr22:51111142..51111149,+p@chr22:51111142..51111149
+
Hg19::chr22:51111154..51111166,+p@chr22:51111154..51111166
+
Hg19::chr22:51111188..51111201,+p@chr22:51111188..51111201
+
Hg19::chr22:51111208..51111238,+p@chr22:51111208..51111238
+


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
adult organism5.56e-60115
anatomical conduit8.07e-26241
neural tube8.52e-2557
neural rod8.52e-2557
future spinal cord8.52e-2557
neural keel8.52e-2557
tube1.87e-24194
anatomical cluster4.63e-22286
regional part of brain1.40e-2059
anterior neural tube6.53e-2042
endothelium1.42e-1918
blood vessel endothelium1.42e-1918
cardiovascular system endothelium1.42e-1918
regional part of forebrain5.44e-1941
forebrain5.44e-1941
future forebrain5.44e-1941
brain1.45e-1769
future brain1.45e-1769
neural plate1.75e-1786
presumptive neural plate1.75e-1786
central nervous system1.89e-1782
neurectoderm6.21e-1690
gray matter9.42e-1634
brain grey matter9.42e-1634
telencephalon2.37e-1534
regional part of telencephalon6.27e-1533
simple squamous epithelium1.21e-1422
regional part of nervous system2.23e-1494
nervous system2.23e-1494
cerebral hemisphere2.59e-1432
squamous epithelium4.47e-1325
regional part of cerebral cortex9.24e-1322
epithelium6.22e-12309
cell layer7.34e-12312
neocortex7.42e-1220
pre-chordal neural plate4.70e-1161
vessel8.64e-1169
endothelial tube1.25e-109
arterial system endothelium1.25e-109
endothelium of artery1.25e-109
cerebral cortex1.64e-1025
pallium1.64e-1025
anterior region of body7.69e-09129
craniocervical region7.69e-09129
splanchnic layer of lateral plate mesoderm9.18e-0984
vasculature1.87e-0879
vascular system1.87e-0879
circulatory system2.00e-08113
head6.68e-08123
epithelial tube8.12e-08118
blood vessel1.21e-0760
epithelial tube open at both ends1.21e-0760
blood vasculature1.21e-0760
vascular cord1.21e-0760
lymphoid system1.67e-0710
cardiovascular system3.31e-07110
nucleus of brain5.80e-079
neural nucleus5.80e-079
brainstem6.94e-078


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
GATA2#2624412.7449317335543.78864877853583e-050.000722444202631922
MAX#414946.452555509007120.0005767613195645490.00485816400145188



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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