Personal tools

Coexpression cluster:C2133

From FANTOM5_SSTAR

Revision as of 18:01, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2133_Mesenchymal_Fibroblast_Smooth_osteoclastoma_Osteoblast_Prostate_leiomyoma



Phase1 CAGE Peaks

Hg19::chr11:46299186..46299195,+p3@CREB3L1
Hg19::chr11:46299199..46299233,+p1@CREB3L1
Hg19::chr11:46299443..46299459,+p4@CREB3L1
Hg19::chr11:46299539..46299620,+p2@CREB3L1


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
somite3.49e-2683
paraxial mesoderm3.49e-2683
presomitic mesoderm3.49e-2683
presumptive segmental plate3.49e-2683
trunk paraxial mesoderm3.49e-2683
presumptive paraxial mesoderm3.49e-2683
dermomyotome1.89e-2370
trunk mesenchyme7.29e-22143
muscle tissue3.84e-2163
musculature3.84e-2163
musculature of body3.84e-2163
skeletal muscle tissue4.01e-2161
striated muscle tissue4.01e-2161
myotome4.01e-2161
multilaminar epithelium2.90e-1982
organism subdivision2.95e-18365
multi-tissue structure7.74e-15347
trunk9.12e-15216
splanchnic layer of lateral plate mesoderm1.92e-1384
unilaminar epithelium3.87e-12138
artery7.17e-1242
arterial blood vessel7.17e-1242
arterial system7.17e-1242
mesenchyme2.04e-11238
entire embryonic mesenchyme2.04e-11238
vasculature6.69e-1179
vascular system6.69e-1179
systemic artery2.41e-1033
systemic arterial system2.41e-1033
multi-cellular organism8.21e-10659
cell layer1.42e-09312
epithelial tube1.57e-09118
blood vessel1.89e-0960
epithelial tube open at both ends1.89e-0960
blood vasculature1.89e-0960
vascular cord1.89e-0960
epithelium3.32e-09309
surface structure5.32e-0995
vessel3.97e-0869
circulatory system3.64e-07113
cardiovascular system3.65e-07110
smooth muscle tissue5.27e-0715
integument5.38e-0745
integumental system5.38e-0745


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.