Personal tools

Coexpression cluster:C2018


Revision as of 05:41, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C2018_Pericytes_Mesenchymal_large_cervical_skeletal_Hair_Fibroblast

Phase1 CAGE Peaks


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.12e-19347
organism subdivision5.04e-15365
organ part5.69e-13219
multi-cellular organism7.90e-13659
anterior region of body7.74e-11129
craniocervical region7.74e-11129
endoderm-derived structure1.08e-10169
presumptive endoderm1.08e-10169
presumptive ectoderm1.16e-10173
ectoderm-derived structure1.63e-10169
digestive system2.81e-09155
digestive tract2.81e-09155
primitive gut2.81e-09155
subdivision of head3.02e-0948
embryonic structure2.67e-08605
developing anatomical structure2.67e-08605
anatomical system4.01e-08625
anatomical group4.93e-08626
germ layer5.04e-08604
embryonic tissue5.04e-08604
presumptive structure5.04e-08604
epiblast (generic)5.04e-08604
sense organ1.58e-0723
adult organism1.68e-07115
entire embryonic mesenchyme2.23e-07238
sensory system2.34e-0724
entire sense organ system2.34e-0724
surface structure5.08e-0795
subdivision of digestive tract6.53e-07129
endodermal part of digestive tract6.53e-07129
neural plate9.43e-0786
presumptive neural plate9.43e-0786
organ segment9.65e-0797

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



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)


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.