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Coexpression cluster:C2162: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2162_gastric_Hepatocyte_Intestinal_liver_Prostate_breast_colon
|full_id=C2162_gastric_Hepatocyte_Intestinal_liver_Prostate_breast_colon
|id=C2162
|id=C2162

Revision as of 14:51, 12 September 2012


Full id: C2162_gastric_Hepatocyte_Intestinal_liver_Prostate_breast_colon



Phase1 CAGE Peaks

Hg19::chr11:72492742..72492753,-p8@STARD10
Hg19::chr11:72492758..72492820,-p2@STARD10
Hg19::chr11:72492878..72492899,-p5@STARD10
Hg19::chr11:72492903..72492966,-p1@STARD10


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 cell1.27e-22254
endodermal cell3.25e-1559
endo-epithelial cell5.75e-1143
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.06e-16169
endoderm4.06e-16169
presumptive endoderm4.06e-16169
trunk region element3.55e-15107
multi-tissue structure1.75e-14347
anatomical conduit7.51e-13241
endo-epithelium1.85e-1282
digestive system2.01e-12155
digestive tract2.01e-12155
primitive gut2.01e-12155
immaterial anatomical entity2.13e-12126
adult organism2.80e-12115
subdivision of digestive tract1.53e-11129
endodermal part of digestive tract1.53e-11129
subdivision of trunk2.18e-11113
multi-cellular organism3.38e-11659
epithelium4.95e-11309
abdomen element5.82e-1155
abdominal segment element5.82e-1155
embryo6.92e-11612
cell layer2.31e-10312
mixed endoderm/mesoderm-derived structure2.52e-10130
embryonic structure7.04e-10605
developing anatomical structure7.04e-10605
germ layer9.88e-10604
embryonic tissue9.88e-10604
presumptive structure9.88e-10604
epiblast (generic)9.88e-10604
anatomical system1.45e-09625
anatomical group1.84e-09626
organ2.05e-09511
organ part3.07e-09219
tube3.21e-09194
anatomical cluster5.59e-09286
organism subdivision6.48e-09365
exocrine gland9.12e-0931
exocrine system9.12e-0931
renal system1.54e-0845
gland2.07e-0859
urinary system structure3.07e-0844
epithelium of foregut-midgut junction6.22e-0825
anatomical boundary6.22e-0825
hepatobiliary system6.22e-0825
foregut-midgut junction6.22e-0825
septum transversum6.22e-0825
mesenchyme7.18e-08238
entire embryonic mesenchyme7.18e-08238
gut epithelium7.70e-0854
foregut8.23e-0898
extraembryonic membrane9.00e-0814
membranous layer9.00e-0814
anatomical space9.44e-08104
sac2.31e-0726
abdominal segment of trunk2.47e-0761
abdomen2.47e-0761
digestive tract diverticulum4.41e-0723
epithelial sac4.70e-0725
kidney8.36e-0727
kidney mesenchyme8.36e-0727
kidney rudiment8.36e-0727
kidney field8.36e-0727
hepatic diverticulum9.02e-0722
liver primordium9.02e-0722
Disease
Ontology termp-valuen
carcinoma9.00e-08106


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
EGR1#195844.988179094810140.001615011500076050.0101291247932046
FOSL1#8061439.7135797163734.01511434669553e-071.93598581373285e-05
FOXA1#316938.311064812039090.002740138182109850.0150334782307927
ZBTB7A#5134147.35190930787590.000342223540015990.00345929968019067
ZNF143#7702413.50087655222793.00867915035614e-050.000619770102138155



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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