Personal tools

Coexpression cluster:C3511

From FANTOM5_SSTAR

Revision as of 19:14, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3511_Mesenchymal_Dendritic_Macrophage_Hepatic_Renal_Osteoblast_Melanocyte



Phase1 CAGE Peaks

Hg19::chr15:73976545..73976624,+p2@CD276
Hg19::chr15:73976691..73976704,+p3@CD276
Hg19::chr15:73976715..73976760,+p1@CD276


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
epithelial tube7.01e-15118
trunk mesenchyme1.23e-14143
multi-cellular organism1.33e-14659
trunk1.03e-13216
vasculature2.93e-1379
vascular system2.93e-1379
splanchnic layer of lateral plate mesoderm1.31e-1284
multilaminar epithelium1.41e-1282
somite3.81e-1283
paraxial mesoderm3.81e-1283
presomitic mesoderm3.81e-1283
presumptive segmental plate3.81e-1283
trunk paraxial mesoderm3.81e-1283
presumptive paraxial mesoderm3.81e-1283
artery1.93e-1142
arterial blood vessel1.93e-1142
arterial system1.93e-1142
dermomyotome4.74e-1170
blood vessel4.87e-1160
epithelial tube open at both ends4.87e-1160
blood vasculature4.87e-1160
vascular cord4.87e-1160
unilaminar epithelium8.34e-11138
skeletal muscle tissue1.42e-1061
striated muscle tissue1.42e-1061
myotome1.42e-1061
anatomical system2.66e-10625
vessel2.70e-1069
anatomical group4.51e-10626
muscle tissue5.30e-1063
musculature5.30e-1063
musculature of body5.30e-1063
cell layer8.51e-10312
embryo1.51e-09612
epithelium1.59e-09309
organism subdivision1.79e-09365
mesenchyme2.63e-09238
entire embryonic mesenchyme2.63e-09238
mesoderm4.80e-09448
mesoderm-derived structure4.80e-09448
presumptive mesoderm4.80e-09448
embryonic structure1.35e-08605
developing anatomical structure1.35e-08605
germ layer1.88e-08604
embryonic tissue1.88e-08604
presumptive structure1.88e-08604
epiblast (generic)1.88e-08604
systemic artery2.35e-0833
systemic arterial system2.35e-0833
cardiovascular system1.19e-07110
multi-tissue structure1.30e-07347
circulatory system2.29e-07113
nephron epithelium3.87e-0716
nephron3.87e-0716
uriniferous tubule3.87e-0716
metanephric mesenchyme3.87e-0716
nephrogenic mesenchyme3.87e-0716
urinary system structure4.56e-0744
renal system7.87e-0745
excretory tube8.68e-0717
mesonephric epithelium8.68e-0717
mesonephric tubule8.68e-0717
nephric duct8.68e-0717
kidney epithelium8.68e-0717
renal duct8.68e-0717
mesonephric duct8.68e-0717
pronephric duct8.68e-0717


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.