Personal tools

Coexpression cluster:C3557

From FANTOM5_SSTAR

Revision as of 15:12, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3557_signet_Prostate_Intestinal_lung_colon_rectal_mesothelioma



Phase1 CAGE Peaks

Hg19::chr16:29840929..29840977,+p@chr16:29840929..29840977
+
Hg19::chr16:29841227..29841239,+p@chr16:29841227..29841239
+
Hg19::chr16:29841250..29841261,+p@chr16:29841250..29841261
+


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
metabolising cell1.15e-1912
endopolyploid cell1.15e-1912
parenchymal cell1.15e-1912
polyploid cell1.15e-1912
hepatocyte1.15e-1912
endodermal cell1.07e-1358
epithelial cell6.49e-09253
epithelial cell of stomach2.41e-073
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract3.42e-18118
epithelium of foregut-midgut junction5.08e-1825
anatomical boundary5.08e-1825
hepatobiliary system5.08e-1825
foregut-midgut junction5.08e-1825
septum transversum5.08e-1825
hepatic diverticulum7.73e-1722
liver primordium7.73e-1722
digestive tract diverticulum4.91e-1623
liver1.29e-1519
digestive gland1.29e-1519
liver bud1.29e-1519
digestive system3.07e-15145
digestive tract3.07e-15145
primitive gut3.07e-15145
epithelial sac1.27e-1425
endoderm-derived structure1.41e-14160
endoderm1.41e-14160
presumptive endoderm1.41e-14160
sac5.35e-1426
gut epithelium6.55e-1354
foregut3.45e-1287
gastrointestinal system4.89e-1125
endo-epithelium2.37e-1082
intestine1.50e-0917
immaterial anatomical entity2.38e-09117
exocrine gland4.53e-0931
exocrine system4.53e-0931
endocrine system4.60e-0945
abdomen element8.36e-0954
abdominal segment element8.36e-0954
trunk region element1.14e-08101
endocrine gland6.89e-0835
abdominal segment of trunk1.03e-0760
abdomen1.03e-0760
primordium1.66e-07160
organ system subdivision5.27e-07223
Disease
Ontology termp-valuen
carcinoma7.24e-19106
cell type cancer4.70e-14143
adenocarcinoma2.13e-1125
signet ring cell adenocarcinoma3.68e-112
cancer2.95e-07235
disease of cellular proliferation5.37e-07239


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#203336.77394172622320.003216880500103790.0167272981105472
FOSL2#2355316.93020060456170.0002060162053171620.00242653958126977
FOXA1#3169311.08141974938550.000734755275698670.00580550054763908
HDAC2#3066313.41562023662630.0004140761399857210.00390727303794441
HNF4A#3172323.13229036295378.07584663437677e-050.00122699061194017
HNF4G#3174328.75342252644684.20470658818262e-050.000756087037471083
RXRA#6256320.07461713913330.0001235730348432220.00165099708148795
SP1#666735.69838137814090.005403962701712170.0246112184111337
USF1#739136.361499277207960.00388404057290560.0189997804868238
USF2#7392312.99219738506960.0004558979393427810.00421209526601387



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.