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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3643_Renal_signet_Hepatic_acute_mesothelioma_Retinal_smallcell
|full_id=C3643_Renal_signet_Hepatic_acute_mesothelioma_Retinal_smallcell
|id=C3643
|id=C3643

Revision as of 16:35, 12 September 2012


Full id: C3643_Renal_signet_Hepatic_acute_mesothelioma_Retinal_smallcell



Phase1 CAGE Peaks

Hg19::chr17:4402141..4402158,+p2@SPNS2
Hg19::chr17:4402161..4402191,+p1@SPNS2
Hg19::chr17:4402213..4402226,+p3@SPNS2


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 organism1.76e-39115
neural tube2.26e-2157
neural rod2.26e-2157
future spinal cord2.26e-2157
neural keel2.26e-2157
central nervous system5.11e-1982
anatomical conduit8.59e-19241
regional part of nervous system4.40e-1894
nervous system4.40e-1894
anterior neural tube1.38e-1742
regional part of forebrain2.32e-1741
forebrain2.32e-1741
future forebrain2.32e-1741
regional part of brain7.01e-1759
neural plate7.88e-1786
presumptive neural plate7.88e-1786
tube2.88e-16194
brain4.59e-1669
future brain4.59e-1669
telencephalon4.72e-1634
gray matter8.78e-1634
brain grey matter8.78e-1634
regional part of telencephalon2.03e-1533
neurectoderm3.07e-1590
cerebral hemisphere9.12e-1532
pre-chordal neural plate2.72e-1361
anatomical cluster3.34e-13286
regional part of cerebral cortex6.87e-1322
neocortex6.96e-1220
head8.87e-12123
anterior region of body8.93e-12129
craniocervical region8.93e-12129
cavitated compound organ1.38e-1132
cerebral cortex3.87e-1125
pallium3.87e-1125
kidney6.24e-1127
kidney mesenchyme6.24e-1127
kidney rudiment6.24e-1127
kidney field6.24e-1127
ectoderm-derived structure1.62e-10169
ectoderm9.05e-10173
presumptive ectoderm9.05e-10173
excretory tube1.18e-0917
mesonephric epithelium1.18e-0917
mesonephric tubule1.18e-0917
nephric duct1.18e-0917
kidney epithelium1.18e-0917
renal duct1.18e-0917
mesonephric duct1.18e-0917
pronephric duct1.18e-0917
mesonephros1.31e-0918
pronephros1.31e-0918
nephrogenic cord1.31e-0918
pronephric mesoderm1.31e-0918
rostral part of nephrogenic cord1.31e-0918
presumptive pronephric mesoderm1.31e-0918
nephron epithelium1.92e-0916
nephron1.92e-0916
uriniferous tubule1.92e-0916
metanephric mesenchyme1.92e-0916
nephrogenic mesenchyme1.92e-0916
intraembryonic coelom2.03e-0921
organ part2.83e-09219
urogenital ridge6.14e-0920
abdomen element4.67e-0855
abdominal segment element4.67e-0855
endothelium4.95e-0818
blood vessel endothelium4.95e-0818
cardiovascular system endothelium4.95e-0818
epithelium1.27e-07309
renal tubule1.61e-0712
nephron tubule1.61e-0712
nephron tubule epithelium1.61e-0712
renal system1.82e-0745
cortex of kidney1.88e-0713
renal parenchyma1.88e-0713
duct2.56e-0726
urinary system structure3.87e-0744
cell layer4.32e-07312


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
E2F6#187635.017155731697390.00791769806886330.0321719825940168
USF1#739136.361499277207960.00388404057290560.019006011966157



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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