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Coexpression cluster:C2372

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Full id: C2372_pancreas_kidney_duodenum_small_temporal_Intestinal_colon



Phase1 CAGE Peaks

Hg19::chr16:3704862..3704880,+p3@DNASE1
Hg19::chr1:43751517..43751532,-p3@C1orf210
Hg19::chr4:70032343..70032354,+p@chr4:70032343..70032354
+
Hg19::chr8:52886175..52886189,+p@chr8:52886175..52886189
+


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 activity0.00317908866125044
GO:0016888endodeoxyribonuclease activity, producing 5'-phosphomonoesters0.0254270943443241
GO:0004520endodeoxyribonuclease activity0.0278031053997779
GO:0006308DNA catabolic process0.0278031053997779
GO:0004536deoxyribonuclease activity0.0291184844105349
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0291184844105349



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 cell of stomach4.19e-103
serous secreting cell2.46e-081
Uber Anatomy
Ontology termp-valuen
gastrointestinal system5.84e-2125
intestine3.80e-1417
small intestine5.11e-144
stomach2.20e-088
food storage organ2.20e-088
epididymis2.29e-081
epithelium of female gonad2.46e-081
subdivision of digestive tract1.04e-07118
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma1.16e-142
ovary epithelial cancer2.46e-081
adenocarcinoma9.00e-0725


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#21011120.9600785340310.008241662461779040.0324836208712258
FOXA2#3170212.31523187633260.009361916285467240.0353399058422638
HNF4G#3174214.37671126322340.006924169980439180.0293023780780051



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.