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Coexpression cluster:C1324: Difference between revisions

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|tf_chipseq_enrich=STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000765955977501647
|tf_chipseq_enrich=STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000765955977501647
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}}
}}

Revision as of 14:49, 26 November 2012


Full id: C1324_Fibroblast_Preadipocyte_basal_migratory_mesenchymal_Smooth_spindle



Phase1 CAGE Peaks

Hg19::chr10:95242223..95242232,-p8@MYOF
Hg19::chr18:56246303..56246344,-p9@ALPK2
Hg19::chr18:56246346..56246375,-p6@ALPK2
Hg19::chr18:56246399..56246415,-p15@ALPK2
Hg19::chr18:56246464..56246503,-p3@ALPK2
Hg19::chr4:77659857..77659874,+p3@SHROOM3


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:0043476pigment accumulation0.00447414122204642
GO:0043482cellular pigment accumulation0.00447414122204642
GO:0033059cellular pigmentation0.00447414122204642
GO:0045176apical protein localization0.00894736048387635
GO:0008105asymmetric protein localization0.00894736048387635
GO:0022603regulation of anatomical structure morphogenesis0.0234757577475775
GO:0008360regulation of cell shape0.0234757577475775
GO:0022604regulation of cell morphogenesis0.0234757577475775
GO:0005912adherens junction0.026824695916118
GO:0016324apical plasma membrane0.030395052708795
GO:0045177apical part of cell0.0349369160994711
GO:0007389pattern specification process0.0461504527999066



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
fibroblast4.37e-2276
skin fibroblast1.56e-1123
multi fate stem cell4.52e-10427
preadipocyte6.34e-1012
somatic stem cell2.57e-09433
mesothelial cell2.91e-0919
stem cell2.29e-08441
animal cell3.60e-08679
eukaryotic cell3.60e-08679
non-terminally differentiated cell1.90e-07106
motile cell9.29e-07386
Uber Anatomy
Ontology termp-valuen
integument4.62e-0946
integumental system4.62e-0946
skin of body9.31e-0941
dense mesenchyme tissue1.17e-0873
somite1.57e-0871
presomitic mesoderm1.57e-0871
presumptive segmental plate1.57e-0871
dermomyotome1.57e-0871
trunk paraxial mesoderm1.57e-0871
paraxial mesoderm3.10e-0872
presumptive paraxial mesoderm3.10e-0872
epithelial vesicle1.42e-0778
multilaminar epithelium4.48e-0783


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
STAT3#677458.766220830961874.28672496720299e-050.000765955977501647



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.