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Coexpression cluster:C1363

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Full id: C1363_pancreas_small_gall_temporal_duodenum_colon_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr12:56624532..56624554,+p2@SLC39A5
Hg19::chr16:3704849..3704860,+p4@DNASE1
Hg19::chr17:202392..202413,+p1@AK125265
Hg19::chr21:37091670..37091681,+p@chr21:37091670..37091681
+
Hg19::chr22:37975952..37975968,-p2@LGALS2
Hg19::chr2:79384252..79384270,-p@chr2:79384252..79384270
-


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:0004530deoxyribonuclease I activity0.0116566584245849



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 cell1.12e-2612
endopolyploid cell1.12e-2612
parenchymal cell1.12e-2612
polyploid cell1.12e-2612
hepatocyte1.12e-2612
endodermal cell6.07e-0958
Uber Anatomy
Ontology termp-valuen
intestine1.02e-3417
gastrointestinal system1.44e-3225
liver1.12e-2519
digestive gland1.12e-2519
liver bud1.12e-2519
digestive tract diverticulum2.76e-2523
large intestine3.34e-2311
epithelium of foregut-midgut junction4.37e-2325
anatomical boundary4.37e-2325
hepatobiliary system4.37e-2325
foregut-midgut junction4.37e-2325
septum transversum4.37e-2325
sac3.98e-2226
hepatic diverticulum6.25e-2222
liver primordium6.25e-2222
subdivision of digestive tract1.36e-20118
epithelial sac4.40e-1925
abdomen element1.34e-1854
abdominal segment element1.34e-1854
digestive system2.19e-17145
digestive tract2.19e-17145
primitive gut2.19e-17145
lower digestive tract2.44e-175
abdominal segment of trunk2.02e-1660
abdomen2.02e-1660
gut epithelium3.78e-1654
endoderm-derived structure2.92e-15160
endoderm2.92e-15160
presumptive endoderm2.92e-15160
exocrine gland4.85e-1531
exocrine system4.85e-1531
colon7.17e-159
endocrine gland4.08e-1335
rectum8.11e-134
endocrine system4.72e-1245
small intestine8.22e-114
trunk region element6.73e-10101
endo-epithelium1.19e-0982
organ system subdivision2.51e-09223
gland1.16e-0859
mesenchyme8.87e-08160
entire embryonic mesenchyme8.87e-08160
subdivision of trunk2.30e-07112
multi-tissue structure4.70e-07342
immaterial anatomical entity7.21e-07117
hindgut7.26e-0719


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#2101180.6400523560210.01233705312615740.0447012729476392
HNF4G#3174419.16894835096452.07234608447467e-050.000458157816927286



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.