Personal tools

Coexpression cluster:C1582

From FANTOM5_SSTAR

Revision as of 14:13, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1582_Preadipocyte_mesothelioma_normal_Adipocyte_gastric_Lens_lung



Phase1 CAGE Peaks

Hg19::chr10:46970474..46970503,-p1@SYT15
Hg19::chr10:46970540..46970551,-p4@SYT15
Hg19::chr10:46970563..46970572,-p3@SYT15
Hg19::chr10:46970573..46970610,-p2@SYT15
Hg19::chr15:81242191..81242201,+p19@KIAA1199


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:0000299integral to membrane of membrane fraction0.00706391360611663
GO:0050954sensory perception of mechanical stimulus0.0387806101493201
GO:0007605sensory perception of sound0.0387806101493201



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.08e-28115
neural plate7.12e-1486
presumptive neural plate7.12e-1486
neurectoderm3.08e-1290
organism subdivision3.18e-12365
regional part of brain4.28e-1259
neural tube5.30e-1157
neural rod5.30e-1157
future spinal cord5.30e-1157
neural keel5.30e-1157
organ2.25e-10511
multi-cellular organism1.57e-09659
anterior region of body2.36e-09129
craniocervical region2.36e-09129
brain2.36e-0969
future brain2.36e-0969
multi-tissue structure4.50e-09347
pre-chordal neural plate7.33e-0961
head7.62e-09123
anatomical cluster1.25e-08286
central nervous system1.49e-0882
anatomical conduit6.10e-08241
tube7.26e-08194
regional part of nervous system7.91e-0894
nervous system7.91e-0894
anterior neural tube1.88e-0742
regional part of forebrain4.63e-0741
forebrain4.63e-0741
future forebrain4.63e-0741


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


No analysis results for this cluster

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.