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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3432_pharyngeal_signet_serous_bile_rectal_clear_mucinous
|full_id=C3432_pharyngeal_signet_serous_bile_rectal_clear_mucinous
|id=C3432
|id=C3432

Revision as of 16:21, 12 September 2012


Full id: C3432_pharyngeal_signet_serous_bile_rectal_clear_mucinous



Phase1 CAGE Peaks

Hg19::chr14:54317486..54317491,-p4@ENST00000418927
Hg19::chr14:54317508..54317523,-p2@ENST00000418927
Hg19::chr14:54317532..54317552,-p1@ENST00000418927


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell8.16e-21254
mesothelial cell3.55e-2019
lining cell7.56e-1357
barrier cell7.56e-1357
squamous epithelial cell4.71e-1062
endodermal cell2.15e-0759
lymphangioblast3.62e-076
endothelial cell of lymphatic vessel3.62e-076
vascular lymphangioblast3.62e-076
Uber Anatomy
Ontology termp-valuen
endo-epithelium8.61e-1582
gut epithelium1.04e-1354
biliary system4.11e-127
biliary tree4.11e-127
biliary bud4.11e-127
endoderm-derived structure2.33e-11169
endoderm2.33e-11169
presumptive endoderm2.33e-11169
mixed endoderm/mesoderm-derived structure2.02e-10130
epithelium of foregut-midgut junction2.33e-1025
anatomical boundary2.33e-1025
hepatobiliary system2.33e-1025
foregut-midgut junction2.33e-1025
septum transversum2.33e-1025
digestive system1.18e-09155
digestive tract1.18e-09155
primitive gut1.18e-09155
subdivision of digestive tract3.44e-09129
endodermal part of digestive tract3.44e-09129
epithelial sac8.12e-0925
sac2.39e-0826
bile duct7.61e-084
digestive system duct7.61e-084
immaterial anatomical entity1.78e-07126
hepatic diverticulum2.82e-0722
liver primordium2.82e-0722
primordium3.58e-07168
abdomen element7.00e-0755
abdominal segment element7.00e-0755
digestive tract diverticulum7.59e-0723
Disease
Ontology termp-valuen
carcinoma1.81e-18106
cell type cancer3.16e-16143
cancer5.69e-13235
disease of cellular proliferation2.43e-12239


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#105137.971147625824820.001974187055288560.0115056987649153
EP300#203336.77394172622320.003216880500103790.0167181420456976
FOS#235338.99795530889440.001372499272417130.00896058332887245
FOXA1#3169311.08141974938550.000734755275698670.00580374423224121
FOXA2#3170324.63046375266526.68983856509345e-050.00107159516855797
HDAC2#3066313.41562023662630.0004140761399857210.00390586145086422
HNF4A#3172323.13229036295378.07584663437677e-050.00122663372112809
JUND#372736.994663941871030.002921845042734990.015643336977403
MAFF#23764356.31535648994525.59409009993116e-060.000168953492176608
MAFK#7975327.10073313782995.02195559325033e-050.000857006568959921
PRDM1#6393131.8309557774614.35536935195671e-072.07988303497488e-05
SP1#666735.69838137814090.005403962701712170.024594058767828
TCF7L2#6934310.77017656313730.0008003181298398380.00612474720908206



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.