Personal tools

Coexpression cluster:C3882

From FANTOM5_SSTAR

Revision as of 16:52, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3882_Skeletal_skeletal_mesenchymal_Hepatic_Neural_astrocytoma_Pericytes



Phase1 CAGE Peaks

Hg19::chr1:156640649..156640659,-p2@NES
Hg19::chr1:156642068..156642092,+p@chr1:156642068..156642092
+
Hg19::chr1:156647192..156647207,-p1@NES


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
cell layer4.03e-29312
epithelium1.15e-27309
anatomical cluster1.14e-26286
anatomical conduit2.18e-25241
tube1.62e-22194
vasculature4.38e-2279
vascular system4.38e-2279
multi-cellular organism1.84e-21659
organism subdivision2.74e-21365
epithelial tube1.54e-20118
anatomical group2.33e-20626
splanchnic layer of lateral plate mesoderm3.15e-2084
anatomical system6.12e-20625
vessel1.59e-1969
multi-tissue structure1.09e-17347
blood vessel1.20e-1760
epithelial tube open at both ends1.20e-1760
blood vasculature1.20e-1760
vascular cord1.20e-1760
circulatory system1.19e-16113
cardiovascular system7.85e-16110
unilaminar epithelium8.29e-16138
trunk mesenchyme1.38e-15143
somite4.34e-1483
paraxial mesoderm4.34e-1483
presomitic mesoderm4.34e-1483
presumptive segmental plate4.34e-1483
trunk paraxial mesoderm4.34e-1483
presumptive paraxial mesoderm4.34e-1483
dermomyotome5.33e-1470
embryo1.15e-13612
muscle tissue1.72e-1263
musculature1.72e-1263
musculature of body1.72e-1263
skeletal muscle tissue2.61e-1261
striated muscle tissue2.61e-1261
myotome2.61e-1261
endothelium6.35e-1218
blood vessel endothelium6.35e-1218
cardiovascular system endothelium6.35e-1218
artery2.27e-1142
arterial blood vessel2.27e-1142
arterial system2.27e-1142
embryonic structure2.70e-11605
developing anatomical structure2.70e-11605
germ layer4.70e-11604
embryonic tissue4.70e-11604
presumptive structure4.70e-11604
epiblast (generic)4.70e-11604
ectoderm-derived structure6.76e-11169
compound organ4.10e-1069
ectoderm5.18e-10173
presumptive ectoderm5.18e-10173
multilaminar epithelium1.06e-0982
central nervous system1.55e-0982
regional part of nervous system2.88e-0994
nervous system2.88e-0994
primary circulatory organ5.55e-0927
simple squamous epithelium6.74e-0922
head7.85e-09123
neural plate1.04e-0886
presumptive neural plate1.04e-0886
systemic artery1.49e-0833
systemic arterial system1.49e-0833
anterior region of body1.74e-08129
craniocervical region1.74e-08129
trunk2.11e-08216
heart3.53e-0824
primitive heart tube3.53e-0824
primary heart field3.53e-0824
anterior lateral plate mesoderm3.53e-0824
heart tube3.53e-0824
heart primordium3.53e-0824
cardiac mesoderm3.53e-0824
cardiogenic plate3.53e-0824
heart rudiment3.53e-0824
squamous epithelium8.18e-0825
mesenchyme1.13e-07238


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.