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Coexpression cluster:C1516

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Full id: C1516_amniotic_Fibroblast_Hair_Amniotic_Placental_Chondrocyte_liposarcoma



Phase1 CAGE Peaks

Hg19::chr3:55515183..55515192,-p12@WNT5A
Hg19::chr3:55515202..55515209,-p15@WNT5A
Hg19::chr3:55515368..55515393,-p1@WNT5A
Hg19::chr3:55515400..55515437,-p3@WNT5A
Hg19::chr3:55515438..55515465,-p4@WNT5A
Hg19::chr3:55515558..55515584,-p18@WNT5A


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
organism subdivision2.41e-17365
somite6.65e-1583
paraxial mesoderm6.65e-1583
presomitic mesoderm6.65e-1583
presumptive segmental plate6.65e-1583
trunk paraxial mesoderm6.65e-1583
presumptive paraxial mesoderm6.65e-1583
multi-tissue structure9.45e-14347
surface structure3.27e-1395
multilaminar epithelium1.94e-1182
dermomyotome2.29e-1170
trunk mesenchyme4.24e-11143
extraembryonic membrane4.61e-1014
membranous layer4.61e-1014
integument1.81e-0945
integumental system1.81e-0945
organ part3.33e-09219
skeletal muscle tissue1.53e-0861
striated muscle tissue1.53e-0861
myotome1.53e-0861
muscle tissue1.93e-0863
musculature1.93e-0863
musculature of body1.93e-0863
multi-cellular organism2.21e-08659
skin of body2.91e-0840
extraembryonic structure4.99e-0824
ectoderm1.06e-07173
presumptive ectoderm1.06e-07173
mesenchyme1.27e-07238
entire embryonic mesenchyme1.27e-07238
subdivision of head2.88e-0748
ectoderm-derived structure2.97e-07169
organ component layer4.56e-0757
trunk7.40e-07216


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#1066465.360256373075034.21437267579784e-050.000755743248433466



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.