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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2378_Hepatocyte_skeletal_heart_liver_medulla_colon_pancreas
|full_id=C2378_Hepatocyte_skeletal_heart_liver_medulla_colon_pancreas
|id=C2378
|id=C2378

Revision as of 15:05, 12 September 2012


Full id: C2378_Hepatocyte_skeletal_heart_liver_medulla_colon_pancreas



Phase1 CAGE Peaks

Hg19::chr16:56717902..56717913,+p@chr16:56717902..56717913
+
Hg19::chr16:56717928..56717945,+p@chr16:56717928..56717945
+
Hg19::chr16:56717951..56717970,+p@chr16:56717951..56717970
+
Hg19::chr16:56717983..56717998,+p@chr16:56717983..56717998
+


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><br>


Cell Type
Ontology termp-valuen
endo-epithelial cell4.14e-0743
endodermal cell4.39e-0759
Uber Anatomy
Ontology termp-valuen
adult organism9.83e-19115
multi-tissue structure2.66e-10347
neural tube6.11e-1057
neural rod6.11e-1057
future spinal cord6.11e-1057
neural keel6.11e-1057
endoderm-derived structure4.53e-09169
endoderm4.53e-09169
presumptive endoderm4.53e-09169
digestive system4.36e-08155
digestive tract4.36e-08155
primitive gut4.36e-08155
subdivision of digestive tract1.83e-07129
endodermal part of digestive tract1.83e-07129
regional part of brain1.97e-0759
respiratory system2.20e-0772
organism subdivision5.69e-07365
central nervous system5.96e-0782
neurectoderm6.20e-0790
gray matter7.98e-0734
brain grey matter7.98e-0734
regional part of forebrain8.27e-0741
forebrain8.27e-0741
future forebrain8.27e-0741


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
CTCF#1066445.360256373075030.001211145381643620.00816754778288102
MAFK#7975320.32554985337240.0001953213688931110.00235067624404559



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.