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Coexpression cluster:C1341: Difference between revisions

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|tf_chipseq_enrich=SMARCC1#6599;2:14.5544531065438:0.00739807938314051:0.0305636080971445
|tf_chipseq_enrich=SMARCC1#6599;2:14.5544531065438:0.00739807938314051:0.0305636080971445
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}}
}}

Revision as of 14:49, 26 November 2012


Full id: C1341_smallcell_small_gall_colon_temporal_signet_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr11:441952..441963,-p2@ANO9
Hg19::chr19:49118307..49118336,-p@chr19:49118307..49118336
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Hg19::chr19:55720851..55720860,-p4@PTPRH
Hg19::chr19:55720862..55720880,-p1@PTPRH
Hg19::chr1:16083098..16083119,+p5@FBLIM1
Hg19::chr1:16083123..16083144,+p4@FBLIM1


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:0019198transmembrane receptor protein phosphatase activity0.0316304946493676
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0316304946493676
GO:0022603regulation of anatomical structure morphogenesis0.0316304946493676
GO:0008360regulation of cell shape0.0316304946493676
GO:0022604regulation of cell morphogenesis0.0316304946493676
GO:0044459plasma membrane part0.0482371433811814



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 cell7.49e-19253
endodermal cell3.21e-0958
endo-epithelial cell2.91e-0742
kidney tubule cell8.35e-0710
nephron tubule epithelial cell8.35e-0710
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.19e-19160
endoderm1.19e-19160
presumptive endoderm1.19e-19160
subdivision of digestive tract2.07e-18118
digestive system4.53e-18145
digestive tract4.53e-18145
primitive gut4.53e-18145
gastrointestinal system1.54e-1425
trunk region element6.19e-14101
immaterial anatomical entity2.93e-12117
anatomical space1.43e-1095
intestine6.91e-1017
foregut9.76e-1087
endo-epithelium7.26e-0982
viscus7.76e-0818
abdomen element1.03e-0754
abdominal segment element1.03e-0754
renal system1.11e-0748
organ2.58e-07503
subdivision of trunk3.70e-07112
urinary system structure4.97e-0747
nephron tubule epithelium8.35e-0710
Disease
Ontology termp-valuen
carcinoma1.94e-14106
adenocarcinoma1.77e-1025
cell type cancer1.95e-09143


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)

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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
SMARCC1#6599214.55445310654380.007398079383140510.0305636080971445



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.