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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4680_Smooth_clear_gastric_Mesothelial_glioma_rectum_melanoma
|full_id=C4680_Smooth_clear_gastric_Mesothelial_glioma_rectum_melanoma
|id=C4680
|id=C4680

Revision as of 17:47, 12 September 2012


Full id: C4680_Smooth_clear_gastric_Mesothelial_glioma_rectum_melanoma



Phase1 CAGE Peaks

Hg19::chr7:27183263..27183284,-p2@HOXA5
Hg19::chr7:27183291..27183324,-p1@HOXA5
Hg19::chr7:27183325..27183338,-p5@HOXA5


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
subdivision of trunk2.09e-15113
cavitated compound organ5.79e-1332
trunk1.24e-12216
epithelial tube7.24e-12118
renal system8.65e-1245
urinary system structure1.75e-1144
kidney4.35e-1127
kidney mesenchyme4.35e-1127
kidney rudiment4.35e-1127
kidney field4.35e-1127
intraembryonic coelom7.43e-1121
mesonephros1.56e-1018
pronephros1.56e-1018
nephrogenic cord1.56e-1018
pronephric mesoderm1.56e-1018
rostral part of nephrogenic cord1.56e-1018
presumptive pronephric mesoderm1.56e-1018
trunk region element2.02e-10107
abdominal segment of trunk2.30e-1061
abdomen2.30e-1061
excretory tube3.60e-1017
mesonephric epithelium3.60e-1017
mesonephric tubule3.60e-1017
nephric duct3.60e-1017
kidney epithelium3.60e-1017
renal duct3.60e-1017
mesonephric duct3.60e-1017
pronephric duct3.60e-1017
mesoderm3.83e-10448
mesoderm-derived structure3.83e-10448
presumptive mesoderm3.83e-10448
urogenital ridge1.11e-0920
nephron epithelium1.68e-0916
nephron1.68e-0916
uriniferous tubule1.68e-0916
metanephric mesenchyme1.68e-0916
nephrogenic mesenchyme1.68e-0916
vessel4.73e-0969
body cavity precursor9.00e-0963
blood vessel9.63e-0960
epithelial tube open at both ends9.63e-0960
blood vasculature9.63e-0960
vascular cord9.63e-0960
anatomical space2.72e-08104
compound organ3.99e-0869
renal tubule4.12e-0812
nephron tubule4.12e-0812
nephron tubule epithelium4.12e-0812
endothelium4.29e-0818
blood vessel endothelium4.29e-0818
cardiovascular system endothelium4.29e-0818
abdomen element5.14e-0855
abdominal segment element5.14e-0855
cortex of kidney6.63e-0813
renal parenchyma6.63e-0813
intermediate mesoderm7.52e-0837
immaterial anatomical entity8.71e-08126
simple squamous epithelium8.74e-0822
vasculature4.93e-0779
vascular system4.93e-0779
duct7.05e-0726
parenchyma7.35e-0717
squamous epithelium7.54e-0725


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285782876353647
CEBPB#105137.971147625824820.001974187055288560.0115806628772906
CTCF#1066435.360256373075030.0064925092527670.028127563523032
EP300#203336.77394172622320.003216880500103790.0168472461413268
MAX#414936.452555509007120.003721913834265510.0187394763986335
MXI1#460139.96157162875930.001011470541259020.00723293199990079
MYC#460935.22228187160940.007020843755740150.0296035326822135
RAD21#5885310.35503389545630.0009004912073565420.00668512945728674
RXRA#6256320.07461713913330.0001235730348432220.00165991565093136
SMC3#9126315.04493284493280.0002935825420371870.00310779111167867
SRF#6722313.79717826216780.0003806615025800190.00376405100056378
STAT3#6774310.51946499715420.0008589184530415310.00645542489329335
USF1#739136.361499277207960.00388404057290560.0191170796641542
USF2#7392312.99219738506960.0004558979393427810.00423193715109952



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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