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Coexpression cluster:C1948

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Full id: C1948_mesenchymal_Smooth_Skeletal_Lens_Keratocytes_cervical_salivary



Phase1 CAGE Peaks

Hg19::chr5:110409038..110409052,+p4@TSLP
Hg19::chr5:110409053..110409100,+p1@TSLP
Hg19::chr5:110409111..110409126,+p2@TSLP
Hg19::chr5:110409130..110409145,+p5@TSLP
Hg19::chr5:110409170..110409189,+p6@TSLP


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
muscle tissue2.57e-1464
musculature2.57e-1464
musculature of body2.57e-1464
skeletal muscle tissue1.37e-1362
striated muscle tissue1.37e-1362
myotome1.37e-1362
paraxial mesoderm7.08e-1372
presumptive paraxial mesoderm7.08e-1372
somite8.52e-1371
presomitic mesoderm8.52e-1371
presumptive segmental plate8.52e-1371
dermomyotome8.52e-1371
trunk paraxial mesoderm8.52e-1371
dense mesenchyme tissue1.94e-1273
multilaminar epithelium8.29e-1183
epithelial vesicle1.56e-1078
trunk mesenchyme1.54e-08122
artery1.99e-0842
arterial blood vessel1.99e-0842
arterial system1.99e-0842
organism subdivision6.52e-08264
mesenchyme2.20e-07160
entire embryonic mesenchyme2.20e-07160
unilaminar epithelium2.22e-07148
germ layer3.51e-07560
germ layer / neural crest3.51e-07560
embryonic tissue3.51e-07560
presumptive structure3.51e-07560
germ layer / neural crest derived structure3.51e-07560
epiblast (generic)3.51e-07560
embryonic structure3.61e-07564
multi-tissue structure8.90e-07342


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#1066455.360256373075030.0002259278299937090.00250166206920196
EGR1#195854.988179094810140.0003237398000590710.00331026639694237
HMGN3#932458.178547723350592.73180911341838e-050.00058273572711663
IRF1#365957.63716375356393.84754333311872e-050.000724938802395069
PAX5#507956.669565531177837.57493746384605e-050.00117133386702194
RAD21#5885510.35503389545638.39503550283973e-060.000229821523690977
SPI1#668858.204323508522732.68916109982495e-050.000575401139325175
ZNF263#1012758.221841637010682.6606316672286e-050.000572227575563608



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.