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Coexpression cluster:C1926: Difference between revisions

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|tf_chipseq_enrich=FOXA1#3169;4:8.86513579950836:0.000307546859137271:0.00316889171482216!GATA3#2625;3:16.3419098143236:0.000467886519508923:0.00430230676272164
|tf_chipseq_enrich=FOXA1#3169;4:8.86513579950836:0.000307546859137271:0.00316889171482216!GATA3#2625;3:16.3419098143236:0.000467886519508923:0.00430230676272164
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}}
}}

Revision as of 15:11, 26 November 2012


Full id: C1926_myxofibrosarcoma_Smooth_mesodermal_Multipotent_Fibroblast_basal_papillary



Phase1 CAGE Peaks

Hg19::chr3:42515138..42515150,-p@chr3:42515138..42515150
-
Hg19::chr3:42515163..42515178,-p@chr3:42515163..42515178
-
Hg19::chr6:72970377..72970387,+p20@RIMS1
Hg19::chr6:72970389..72970411,+p6@RIMS1
Hg19::chr6:72970412..72970435,+p11@RIMS1


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>


Uber Anatomy
Ontology termp-valuen
brain vasculature2.80e-195
vasculature1.13e-1378
vascular system1.13e-1378
cardiovascular system8.38e-12109
umbilical vein9.79e-125
circulatory system2.44e-11112
umbilical blood vessel7.86e-109
vein1.01e-099
venous blood vessel1.01e-099
venous system1.01e-099
vascular plexus7.35e-092
ventricle of nervous system7.35e-092
choroid plexus7.35e-092
brain ventricle7.35e-092
ventricular system of brain7.35e-092
ventricular system of central nervous system7.35e-092
vasculature of organ1.47e-0811
vessel2.31e-0868
meninx1.05e-072
membrane organ1.05e-072
meningeal cluster1.05e-072
epithelial tube open at both ends2.38e-0759
blood vessel2.38e-0759
blood vasculature2.38e-0759
vascular cord2.38e-0759
splanchnic layer of lateral plate mesoderm3.21e-0783
blood vessel endothelium9.99e-0718
endothelium9.99e-0718
cardiovascular system endothelium9.99e-0718


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)

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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
FOXA1#316948.865135799508360.0003075468591372710.00316889171482216
GATA3#2625316.34190981432360.0004678865195089230.00430230676272164



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.