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Coexpression cluster:C4187: Difference between revisions

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|full_id=C4187_colon_gastrointestinal_small_hepatoblastoma_rectum_stomach_duodenum
|full_id=C4187_colon_gastrointestinal_small_hepatoblastoma_rectum_stomach_duodenum
|id=C4187
|id=C4187
|ontology_enrichment_celltype=CL:0000181!1.85e-07!12;CL:0000417!1.85e-07!12;CL:0000668!1.85e-07!12;CL:0000414!1.85e-07!12;CL:0000412!1.85e-07!12;CL:0000182!1.85e-07!12
|ontology_enrichment_celltype=CL:0002322!6.63e-08!5
|ontology_enrichment_disease=DOID:3119!7.82e-07!14
|ontology_enrichment_disease=DOID:3493!3.25e-09!2;DOID:3119!2.56e-07!14
|ontology_enrichment_uberon=UBERON:0004921!6.54e-11!129;UBERON:0004185!6.54e-11!129;UBERON:0005409!2.36e-10!35;UBERON:0000160!1.50e-09!27;UBERON:0009854!4.54e-09!23;UBERON:0001007!5.24e-09!155;UBERON:0001555!5.24e-09!155;UBERON:0007026!5.24e-09!155;UBERON:0004119!2.22e-08!169;UBERON:0000925!2.22e-08!169;UBERON:0006595!2.22e-08!169;UBERON:0009497!4.48e-08!25;UBERON:0000015!4.48e-08!25;UBERON:0002423!4.48e-08!25;UBERON:0006235!4.48e-08!25;UBERON:0004161!4.48e-08!25;UBERON:0008835!5.90e-08!22;UBERON:0003894!5.90e-08!22;UBERON:0000059!9.23e-08!11;UBERON:0009856!1.21e-07!26;UBERON:0003929!2.14e-07!54;UBERON:0002417!4.13e-07!61;UBERON:0000916!4.13e-07!61;UBERON:0000466!5.01e-07!126;UBERON:0000077!5.54e-07!130;UBERON:0002107!9.61e-07!19;UBERON:0006925!9.61e-07!19;UBERON:0008836!9.61e-07!19
|ontology_enrichment_uberon=UBERON:0005409!2.21e-29!25;UBERON:0000160!3.32e-27!17;UBERON:0000059!1.07e-18!11;UBERON:0004907!4.98e-14!5;UBERON:0004921!4.66e-13!118;UBERON:0001155!4.42e-12!9;UBERON:0001007!1.01e-10!145;UBERON:0001555!1.01e-10!145;UBERON:0007026!1.01e-10!145;UBERON:0001052!2.02e-10!4;UBERON:0004119!3.27e-09!160;UBERON:0000925!3.27e-09!160;UBERON:0006595!3.27e-09!160;UBERON:0002108!1.63e-08!4;UBERON:0001046!2.30e-07!19
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223169106027411
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223169106027411
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}}
}}

Revision as of 15:44, 19 October 2012


Full id: C4187_colon_gastrointestinal_small_hepatoblastoma_rectum_stomach_duodenum



Phase1 CAGE Peaks

Hg19::chr2:219925637..219925649,-p1@IHH
Hg19::chr2:219925704..219925721,-p3@IHH
Hg19::chr2:219925783..219925786,-p@chr2:219925783..219925786
-


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
embryonic stem cell6.63e-085
Uber Anatomy
Ontology termp-valuen
gastrointestinal system2.21e-2925
intestine3.32e-2717
large intestine1.07e-1811
lower digestive tract4.98e-145
subdivision of digestive tract4.66e-13118
colon4.42e-129
digestive system1.01e-10145
digestive tract1.01e-10145
primitive gut1.01e-10145
rectum2.02e-104
endoderm-derived structure3.27e-09160
endoderm3.27e-09160
presumptive endoderm3.27e-09160
small intestine1.63e-084
hindgut2.30e-0719
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma3.25e-092
gastrointestinal system cancer2.56e-0714


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
SUZ12#23512350.11578091106297.93834897779404e-060.000223169106027411



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.