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Coexpression cluster:C794

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Full id: C794_small_signet_adenocarcinoma_colon_Hepatocyte_gall_liver



Phase1 CAGE Peaks

Hg19::chr11:123461510..123461537,+p@chr11:123461510..123461537
+
Hg19::chr12:49741821..49741836,+p@chr12:49741821..49741836
+
Hg19::chr20:60987744..60987756,-p@chr20:60987744..60987756
-
Hg19::chr3:149192427..149192438,+p2@TM4SF4
Hg19::chr7:155754002..155754015,+p@chr7:155754002..155754015
+
Hg19::chr7:155754027..155754046,+p@chr7:155754027..155754046
+
Hg19::chr7:15707836..15707857,+p1@ENST00000451240
p1@uc003ste.2
Hg19::chr7:44580861..44580912,-p1@NPC1L1
Hg19::chr7:44580918..44580934,-p2@NPC1L1
Hg19::chr9:130877633..130877641,-p@chr9:130877633..130877641
-


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:0030299cholesterol absorption0.0135790157865837
GO:0044241lipid digestion0.0135790157865837
GO:0050892intestinal absorption0.0135790157865837
GO:0008158hedgehog receptor activity0.0135790157865837
GO:0015918sterol transport0.0135790157865837
GO:0030301cholesterol transport0.0135790157865837
GO:0022600digestive system process0.0135790157865837
GO:0006695cholesterol biosynthetic process0.0156323542899154
GO:0016126sterol biosynthetic process0.01833980188362
GO:0006487protein amino acid N-linked glycosylation0.0249859883709692
GO:0016324apical plasma membrane0.0249859883709692
GO:0044459plasma membrane part0.0249859883709692
GO:0008203cholesterol metabolic process0.0249859883709692
GO:0042157lipoprotein metabolic process0.0249859883709692
GO:0045177apical part of cell0.0249859883709692
GO:0009058biosynthetic process0.0249859883709692
GO:0006694steroid biosynthetic process0.0249859883709692
GO:0016125sterol metabolic process0.0249859883709692
GO:0007586digestion0.0249859883709692
GO:0030659cytoplasmic vesicle membrane0.0254574086141063
GO:0044433cytoplasmic vesicle part0.0254574086141063
GO:0012506vesicle membrane0.0256606148778984
GO:0006869lipid transport0.0293140852477049
GO:0006486protein amino acid glycosylation0.0349355291417189
GO:0043413biopolymer glycosylation0.0349355291417189
GO:0009101glycoprotein biosynthetic process0.0349355291417189
GO:0009100glycoprotein metabolic process0.0374071710405309
GO:0005886plasma membrane0.0374071710405309
GO:0008202steroid metabolic process0.0374071710405309
GO:0008285negative regulation of cell proliferation0.0374071710405309



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>


Cell Type
Ontology termp-valuen
metabolising cell1.61e-2712
endopolyploid cell1.61e-2712
parenchymal cell1.61e-2712
polyploid cell1.61e-2712
hepatocyte1.61e-2712
endodermal cell3.47e-1058
intestinal epithelial cell8.25e-084
Uber Anatomy
Ontology termp-valuen
epithelium of foregut-midgut junction6.64e-2625
anatomical boundary6.64e-2625
hepatobiliary system6.64e-2625
foregut-midgut junction6.64e-2625
septum transversum6.64e-2625
hepatic diverticulum7.26e-2422
liver primordium7.26e-2422
intestine1.00e-2317
small intestine6.95e-234
digestive tract diverticulum9.07e-2323
liver3.58e-2219
digestive gland3.58e-2219
liver bud3.58e-2219
epithelial sac7.72e-2125
gastrointestinal system2.81e-2025
sac5.52e-2026
gut epithelium5.09e-1954
abdomen element3.95e-1654
abdominal segment element3.95e-1654
subdivision of digestive tract2.76e-15118
abdominal segment of trunk2.68e-1460
abdomen2.68e-1460
digestive system2.01e-13145
digestive tract2.01e-13145
primitive gut2.01e-13145
exocrine gland3.63e-1331
exocrine system3.63e-1331
endoderm-derived structure7.92e-12160
endoderm7.92e-12160
presumptive endoderm7.92e-12160
endo-epithelium1.07e-1182
endocrine gland1.56e-1135
endocrine system5.11e-1145
duodenum3.75e-102
trunk region element4.70e-09101
gland4.79e-0859
hepatopancreatic ampulla7.16e-081
extrahepatic bile duct7.16e-081
common bile duct7.16e-081
duodenal papilla7.16e-081
intestinal mucosa8.25e-084
wall of intestine8.25e-084
gastrointestinal system mucosa8.25e-084
gastrointestinal system epithelium8.25e-084
intestinal epithelium8.25e-084
colon2.05e-079
organ system subdivision2.62e-07223


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
EP300#203353.38697086311160.009216261698114180.0348391905128618
FOSL2#235546.772080241824680.001913955163860850.0112608621124705
HNF4A#3172511.56614518147683.16474693899284e-050.00063549895320414
HNF4G#3174411.50136901057870.0002593045920322360.00278129940302503
MAFF#23764211.2630712979890.01290318508912210.0464064102594036
SREBF2#6721287.38865248226950.0002323059271552280.00255306731833788



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.