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Coexpression cluster:C3482: Difference between revisions

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|tf_chipseq_enrich=MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191085751474971
|tf_chipseq_enrich=MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191085751474971
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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3482_Fibroblast_Hair_Preadipocyte_Smooth_mesenchymal_Adipocyte_Keratocytes



Phase1 CAGE Peaks

Hg19::chr15:39534820..39534834,+p@chr15:39534820..39534834
+
Hg19::chr1:215130919..215130936,+p@chr1:215130919..215130936
+
Hg19::chr8:119800776..119800782,+p@chr8:119800776..119800782
+


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
skin fibroblast1.31e-2523
fibroblast6.89e-2476
preadipocyte of the breast8.61e-133
receptor cell4.22e-106
sensory epithelial cell4.22e-106
olfactory epithelial cell4.22e-106
multi fate stem cell2.41e-09427
adipocyte of breast4.19e-092
somatic stem cell4.47e-09433
stem cell9.94e-09441
preadipocyte2.68e-0812
somatic cell2.47e-07588
Uber Anatomy
Ontology termp-valuen
skin of body1.32e-2041
integument6.06e-1846
integumental system6.06e-1846
surface structure1.52e-1399
breast6.42e-1010
chest5.52e-0911
Disease
Ontology termp-valuen
musculoskeletal system disease1.54e-195
myotonic disease1.54e-195
muscle tissue disease1.54e-195
myopathy1.54e-195
muscular disease1.54e-195
myotonic dystrophy1.54e-195


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
MAFK#7975218.06715542521990.003983674744936810.0191085751474971



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.