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Coexpression cluster:C4362

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Full id: C4362_Multipotent_bone_basal_amniotic_Myoblast_Nucleus_Smooth



Phase1 CAGE Peaks

Hg19::chr4:114900167..114900191,-p4@ARSJ
Hg19::chr4:114900781..114900830,-p1@ARSJ
Hg19::chr4:114900831..114900844,-p3@ARSJ


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
vasculature2.21e-2778
vascular system2.21e-2778
vessel3.20e-2468
epithelial tube open at both ends3.93e-2359
blood vessel3.93e-2359
blood vasculature3.93e-2359
vascular cord3.93e-2359
unilaminar epithelium9.64e-23148
splanchnic layer of lateral plate mesoderm3.25e-2283
artery2.14e-2142
arterial blood vessel2.14e-2142
arterial system2.14e-2142
multilaminar epithelium2.80e-2183
somite5.81e-2171
presomitic mesoderm5.81e-2171
presumptive segmental plate5.81e-2171
dermomyotome5.81e-2171
trunk paraxial mesoderm5.81e-2171
dense mesenchyme tissue6.04e-2173
epithelial vesicle8.85e-2178
paraxial mesoderm1.36e-2072
presumptive paraxial mesoderm1.36e-2072
epithelial tube1.09e-19117
mesenchyme1.37e-19160
entire embryonic mesenchyme1.37e-19160
organism subdivision1.41e-19264
skeletal muscle tissue1.27e-1862
striated muscle tissue1.27e-1862
myotome1.27e-1862
cardiovascular system2.24e-18109
muscle tissue2.86e-1864
musculature2.86e-1864
musculature of body2.86e-1864
cell layer3.62e-18309
epithelium4.82e-18306
circulatory system1.65e-17112
trunk mesenchyme4.09e-17122
anatomical cluster2.23e-16373
systemic artery2.34e-1633
systemic arterial system2.34e-1633
multi-tissue structure1.91e-15342
surface structure2.67e-1599
anatomical conduit2.48e-14240
anatomical system1.33e-13624
multi-cellular organism1.66e-13656
anatomical group2.28e-13625
trunk2.41e-13199
aorta3.67e-1021
aortic system3.67e-1021
tube3.18e-08192
head6.24e-0856
developing anatomical structure1.43e-07581
embryo2.87e-07592
subdivision of skeletal system3.59e-0716
simple squamous epithelium3.67e-0722
blood vessel endothelium3.86e-0718
endothelium3.86e-0718
cardiovascular system endothelium3.86e-0718


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0280612139484247
NR3C1#290829.982015554115360.01278474365547170.0460645084742224



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.