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Coexpression cluster:C4645: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004638!8.21e-29!18;UBERON:0001986!8.21e-29!18;UBERON:0004852!8.21e-29!18;UBERON:0000487!1.48e-22!22;UBERON:0006914!3.42e-19!25;UBERON:0002049!8.06e-16!78;UBERON:0007798!8.06e-16!78;UBERON:0000490!1.23e-15!148;UBERON:0003915!4.02e-13!9;UBERON:0004700!4.02e-13!9;UBERON:0001917!4.02e-13!9;UBERON:0000055!6.60e-12!68;UBERON:0001638!2.55e-10!9;UBERON:0003920!2.55e-10!9;UBERON:0004582!2.55e-10!9;UBERON:0007503!5.84e-10!78;UBERON:0002329!1.24e-09!71;UBERON:0003059!1.24e-09!71;UBERON:0007282!1.24e-09!71;UBERON:0004290!1.24e-09!71;UBERON:0009618!1.24e-09!71;UBERON:0003077!2.10e-09!72;UBERON:0007285!2.10e-09!72;UBERON:0010260!2.89e-09!9;UBERON:0007524!3.50e-09!73;UBERON:0004535!9.23e-09!109;UBERON:0007500!1.17e-08!59;UBERON:0001981!1.17e-08!59;UBERON:0004537!1.17e-08!59;UBERON:0006965!1.17e-08!59;UBERON:0001009!2.64e-08!112;UBERON:0000486!5.07e-08!83;UBERON:0001134!7.83e-07!62;UBERON:0002036!7.83e-07!62;UBERON:0003082!7.83e-07!62;UBERON:0002066!9.70e-07!5
|ontology_enrichment_uberon=UBERON:0004638!8.21e-29!18;UBERON:0001986!8.21e-29!18;UBERON:0004852!8.21e-29!18;UBERON:0000487!1.48e-22!22;UBERON:0006914!3.42e-19!25;UBERON:0002049!8.06e-16!78;UBERON:0007798!8.06e-16!78;UBERON:0000490!1.23e-15!148;UBERON:0003915!4.02e-13!9;UBERON:0004700!4.02e-13!9;UBERON:0001917!4.02e-13!9;UBERON:0000055!6.60e-12!68;UBERON:0001638!2.55e-10!9;UBERON:0003920!2.55e-10!9;UBERON:0004582!2.55e-10!9;UBERON:0007503!5.84e-10!78;UBERON:0002329!1.24e-09!71;UBERON:0003059!1.24e-09!71;UBERON:0007282!1.24e-09!71;UBERON:0004290!1.24e-09!71;UBERON:0009618!1.24e-09!71;UBERON:0003077!2.10e-09!72;UBERON:0007285!2.10e-09!72;UBERON:0010260!2.89e-09!9;UBERON:0007524!3.50e-09!73;UBERON:0004535!9.23e-09!109;UBERON:0007500!1.17e-08!59;UBERON:0001981!1.17e-08!59;UBERON:0004537!1.17e-08!59;UBERON:0006965!1.17e-08!59;UBERON:0001009!2.64e-08!112;UBERON:0000486!5.07e-08!83;UBERON:0001134!7.83e-07!62;UBERON:0002036!7.83e-07!62;UBERON:0003082!7.83e-07!62;UBERON:0002066!9.70e-07!5
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}}
}}

Revision as of 16:52, 26 November 2012


Full id: C4645_Endothelial_epithelioid_Smooth_schwannoma_mesenchymal_Skeletal_mesodermal



Phase1 CAGE Peaks

Hg19::chr7:115915044..115915047,-p@chr7:115915044..115915047
-
Hg19::chr7:115967923..115967936,-p2@ENST00000444244
Hg19::chr7:115967941..115967974,-p1@ENST00000444244


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>

Cell Type
Ontology termp-valuen
endothelial cell of vascular tree1.52e-3524
blood vessel endothelial cell8.21e-2918
embryonic blood vessel endothelial progenitor cell8.21e-2918
endothelial cell1.46e-2536
mesodermal cell3.54e-25121
meso-epithelial cell1.84e-2045
lining cell1.31e-1958
barrier cell1.31e-1958
embryonic cell6.72e-14250
endothelial cell of artery4.02e-139
vein endothelial cell1.63e-126
skin fibroblast1.34e-0923
squamous epithelial cell1.53e-0963
somatic cell4.38e-09588
aortic endothelial cell1.47e-086
lymphangioblast2.28e-086
endothelial cell of lymphatic vessel2.28e-086
vascular lymphangioblast2.28e-086
fibroblast of dermis6.39e-086
muscle precursor cell1.19e-0758
myoblast1.19e-0758
multi-potent skeletal muscle stem cell1.19e-0758
muscle cell1.67e-0755
endothelial cell of umbilical vein2.65e-073
animal cell4.70e-07679
eukaryotic cell4.70e-07679
non-terminally differentiated cell6.03e-07106
cell of skeletal muscle9.39e-079
Uber Anatomy
Ontology termp-valuen
blood vessel endothelium8.21e-2918
endothelium8.21e-2918
cardiovascular system endothelium8.21e-2918
simple squamous epithelium1.48e-2222
squamous epithelium3.42e-1925
vasculature8.06e-1678
vascular system8.06e-1678
unilaminar epithelium1.23e-15148
endothelial tube4.02e-139
arterial system endothelium4.02e-139
endothelium of artery4.02e-139
vessel6.60e-1268
vein2.55e-109
venous blood vessel2.55e-109
venous system2.55e-109
epithelial vesicle5.84e-1078
somite1.24e-0971
presomitic mesoderm1.24e-0971
presumptive segmental plate1.24e-0971
dermomyotome1.24e-0971
trunk paraxial mesoderm1.24e-0971
paraxial mesoderm2.10e-0972
presumptive paraxial mesoderm2.10e-0972
umbilical blood vessel2.89e-099
dense mesenchyme tissue3.50e-0973
cardiovascular system9.23e-09109
epithelial tube open at both ends1.17e-0859
blood vessel1.17e-0859
blood vasculature1.17e-0859
vascular cord1.17e-0859
circulatory system2.64e-08112
multilaminar epithelium5.07e-0883
skeletal muscle tissue7.83e-0762
striated muscle tissue7.83e-0762
myotome7.83e-0762
umbilical vein9.70e-075


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.

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