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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3631_signet_liver_Hepatocyte_lung_gastrointestinal_duodenum_gall
|full_id=C3631_signet_liver_Hepatocyte_lung_gastrointestinal_duodenum_gall
|gostat_on_coexpression_clusters=GO:0005916!fascia adherens!0.00800506168636512!3728$GO:0009898!internal side of plasma membrane!0.00800506168636512!3728$GO:0005624!membrane fraction!0.00800506168636512!3728;7104$GO:0030057!desmosome!0.00800506168636512!3728$GO:0000267!cell fraction!0.00800506168636512!3728;7104$GO:0005913!cell-cell adherens junction!0.00800506168636512!3728$GO:0030018!Z disc!0.00800506168636512!3728$GO:0031674!I band!0.00850500241229507!3728$GO:0014704!intercalated disc!0.0166161071869071!3728$GO:0030017!sarcomere!0.0166161071869071!3728$GO:0030016!myofibril!0.0166161071869071!3728$GO:0006487!protein amino acid N-linked glycosylation!0.0166161071869071!7104$GO:0005912!adherens junction!0.0166161071869071!3728$GO:0044449!contractile fiber part!0.0170648948467576!3728$GO:0043292!contractile fiber!0.0170648948467576!3728$GO:0044459!plasma membrane part!0.0192194868159395!3728;7104$GO:0043296!apical junction complex!0.0233168186805186!3728$GO:0016327!apicolateral plasma membrane!0.0233168186805186!3728$GO:0005911!intercellular junction!0.0330299548248979!3728$GO:0006486!protein amino acid glycosylation!0.0330299548248979!7104$GO:0043413!biopolymer glycosylation!0.0330299548248979!7104$GO:0009101!glycoprotein biosynthetic process!0.0330299548248979!7104$GO:0009100!glycoprotein metabolic process!0.0357413648296294!7104$GO:0005886!plasma membrane!0.0357413648296294!3728;7104$GO:0008285!negative regulation of cell proliferation!0.0359061114950822!7104$GO:0005625!soluble fraction!0.0359061114950822!3728$GO:0015629!actin cytoskeleton!0.0436974359223854!3728$GO:0016337!cell-cell adhesion!0.0493596312651508!3728
|gostat_on_coexpression_clusters=GO:0005916!fascia adherens!0.00800506168636512!3728$GO:0009898!internal side of plasma membrane!0.00800506168636512!3728$GO:0005624!membrane fraction!0.00800506168636512!3728;7104$GO:0030057!desmosome!0.00800506168636512!3728$GO:0000267!cell fraction!0.00800506168636512!3728;7104$GO:0005913!cell-cell adherens junction!0.00800506168636512!3728$GO:0030018!Z disc!0.00800506168636512!3728$GO:0031674!I band!0.00850500241229507!3728$GO:0014704!intercalated disc!0.0166161071869071!3728$GO:0030017!sarcomere!0.0166161071869071!3728$GO:0030016!myofibril!0.0166161071869071!3728$GO:0006487!protein amino acid N-linked glycosylation!0.0166161071869071!7104$GO:0005912!adherens junction!0.0166161071869071!3728$GO:0044449!contractile fiber part!0.0170648948467576!3728$GO:0043292!contractile fiber!0.0170648948467576!3728$GO:0044459!plasma membrane part!0.0192194868159395!3728;7104$GO:0043296!apical junction complex!0.0233168186805186!3728$GO:0016327!apicolateral plasma membrane!0.0233168186805186!3728$GO:0005911!intercellular junction!0.0330299548248979!3728$GO:0006486!protein amino acid glycosylation!0.0330299548248979!7104$GO:0043413!biopolymer glycosylation!0.0330299548248979!7104$GO:0009101!glycoprotein biosynthetic process!0.0330299548248979!7104$GO:0009100!glycoprotein metabolic process!0.0357413648296294!7104$GO:0005886!plasma membrane!0.0357413648296294!3728;7104$GO:0008285!negative regulation of cell proliferation!0.0359061114950822!7104$GO:0005625!soluble fraction!0.0359061114950822!3728$GO:0015629!actin cytoskeleton!0.0436974359223854!3728$GO:0016337!cell-cell adhesion!0.0493596312651508!3728

Revision as of 16:35, 12 September 2012


Full id: C3631_signet_liver_Hepatocyte_lung_gastrointestinal_duodenum_gall



Phase1 CAGE Peaks

Hg19::chr17:39928985..39929000,-p16@JUP
Hg19::chr3:149193560..149193572,+p3@TM4SF4
Hg19::chr3:149193636..149193643,+p10@TM4SF4


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


GO IDGO nameFDR corrected p-value
GO:0005916fascia adherens0.00800506168636512
GO:0009898internal side of plasma membrane0.00800506168636512
GO:0005624membrane fraction0.00800506168636512
GO:0030057desmosome0.00800506168636512
GO:0000267cell fraction0.00800506168636512
GO:0005913cell-cell adherens junction0.00800506168636512
GO:0030018Z disc0.00800506168636512
GO:0031674I band0.00850500241229507
GO:0014704intercalated disc0.0166161071869071
GO:0030017sarcomere0.0166161071869071
GO:0030016myofibril0.0166161071869071
GO:0006487protein amino acid N-linked glycosylation0.0166161071869071
GO:0005912adherens junction0.0166161071869071
GO:0044449contractile fiber part0.0170648948467576
GO:0043292contractile fiber0.0170648948467576
GO:0044459plasma membrane part0.0192194868159395
GO:0043296apical junction complex0.0233168186805186
GO:0016327apicolateral plasma membrane0.0233168186805186
GO:0005911intercellular junction0.0330299548248979
GO:0006486protein amino acid glycosylation0.0330299548248979
GO:0043413biopolymer glycosylation0.0330299548248979
GO:0009101glycoprotein biosynthetic process0.0330299548248979
GO:0009100glycoprotein metabolic process0.0357413648296294
GO:0005886plasma membrane0.0357413648296294
GO:0008285negative regulation of cell proliferation0.0359061114950822
GO:0005625soluble fraction0.0359061114950822
GO:0015629actin cytoskeleton0.0436974359223854
GO:0016337cell-cell adhesion0.0493596312651508



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
metabolising cell2.95e-1712
endopolyploid cell2.95e-1712
parenchymal cell2.95e-1712
polyploid cell2.95e-1712
hepatocyte2.95e-1712
Uber Anatomy
Ontology termp-valuen
epithelium of foregut-midgut junction1.58e-2025
anatomical boundary1.58e-2025
hepatobiliary system1.58e-2025
foregut-midgut junction1.58e-2025
septum transversum1.58e-2025
epithelial sac2.85e-2025
hepatic diverticulum4.33e-2022
liver primordium4.33e-2022
liver7.66e-2019
digestive gland7.66e-2019
liver bud7.66e-2019
sac2.29e-1926
digestive tract diverticulum4.34e-1923
gut epithelium1.63e-1754
endo-epithelium6.95e-1782
immune organ2.94e-1626
endocrine gland2.24e-1335
subdivision of digestive tract1.83e-12129
endodermal part of digestive tract1.83e-12129
digestive system4.14e-12155
digestive tract4.14e-12155
primitive gut4.14e-12155
abdomen element1.48e-1155
abdominal segment element1.48e-1155
abdominal segment of trunk1.70e-1161
abdomen1.70e-1161
endocrine system1.83e-1145
endoderm-derived structure2.13e-11169
endoderm2.13e-11169
presumptive endoderm2.13e-11169
exocrine gland3.55e-1131
exocrine system3.55e-1131
mixed endoderm/mesoderm-derived structure2.27e-09130
gland3.99e-0959
foregut1.71e-0898
trunk region element2.87e-08107
subdivision of trunk1.57e-07113
immaterial anatomical entity3.44e-07126
gastrointestinal system7.62e-0735
Disease
Ontology termp-valuen
clear cell adenocarcinoma5.78e-082
carcinoma1.84e-07106


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
ESRRA#21011161.2801047120420.006187620080219560.0273489717532714



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.