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Coexpression cluster:C2007: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001134!1.19e-18!62;UBERON:0002036!1.19e-18!62;UBERON:0003082!1.19e-18!62;UBERON:0002385!2.09e-18!64;UBERON:0001015!2.09e-18!64;UBERON:0000383!2.09e-18!64;UBERON:0002329!7.12e-18!71;UBERON:0003059!7.12e-18!71;UBERON:0007282!7.12e-18!71;UBERON:0004290!7.12e-18!71;UBERON:0009618!7.12e-18!71;UBERON:0003077!2.31e-17!72;UBERON:0007285!2.31e-17!72;UBERON:0007524!7.21e-17!73;UBERON:0000486!2.19e-16!83;UBERON:0007503!2.78e-15!78;UBERON:0003102!5.43e-13!99;UBERON:0005256!1.99e-11!122;UBERON:0001637!2.11e-11!42;UBERON:0003509!2.11e-11!42;UBERON:0004572!2.11e-11!42;UBERON:0004573!2.33e-10!33;UBERON:0004571!2.33e-10!33;UBERON:0003104!9.67e-09!160;UBERON:0009142!9.67e-09!160;UBERON:0000490!4.68e-08!148;UBERON:0007500!7.94e-08!59;UBERON:0001981!7.94e-08!59;UBERON:0004537!7.94e-08!59;UBERON:0006965!7.94e-08!59;UBERON:0002199!1.17e-07!46;UBERON:0002416!1.17e-07!46;UBERON:0004872!3.50e-07!83;UBERON:0001135!3.96e-07!15;UBERON:0000475!4.19e-07!264;UBERON:0002097!9.08e-07!41
|ontology_enrichment_uberon=UBERON:0001134!1.19e-18!62;UBERON:0002036!1.19e-18!62;UBERON:0003082!1.19e-18!62;UBERON:0002385!2.09e-18!64;UBERON:0001015!2.09e-18!64;UBERON:0000383!2.09e-18!64;UBERON:0002329!7.12e-18!71;UBERON:0003059!7.12e-18!71;UBERON:0007282!7.12e-18!71;UBERON:0004290!7.12e-18!71;UBERON:0009618!7.12e-18!71;UBERON:0003077!2.31e-17!72;UBERON:0007285!2.31e-17!72;UBERON:0007524!7.21e-17!73;UBERON:0000486!2.19e-16!83;UBERON:0007503!2.78e-15!78;UBERON:0003102!5.43e-13!99;UBERON:0005256!1.99e-11!122;UBERON:0001637!2.11e-11!42;UBERON:0003509!2.11e-11!42;UBERON:0004572!2.11e-11!42;UBERON:0004573!2.33e-10!33;UBERON:0004571!2.33e-10!33;UBERON:0003104!9.67e-09!160;UBERON:0009142!9.67e-09!160;UBERON:0000490!4.68e-08!148;UBERON:0007500!7.94e-08!59;UBERON:0001981!7.94e-08!59;UBERON:0004537!7.94e-08!59;UBERON:0006965!7.94e-08!59;UBERON:0002199!1.17e-07!46;UBERON:0002416!1.17e-07!46;UBERON:0004872!3.50e-07!83;UBERON:0001135!3.96e-07!15;UBERON:0000475!4.19e-07!264;UBERON:0002097!9.08e-07!41
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}}
}}

Revision as of 15:14, 26 November 2012


Full id: C2007_liposarcoma_Fibroblast_Myoblast_Preadipocyte_mesenchymal_basal_Smooth



Phase1 CAGE Peaks

Hg19::chr8:122625184..122625186,-p@chr8:122625184..122625186
-
Hg19::chr8:122653259..122653278,+p4@HAS2-AS1
Hg19::chr8:122653465..122653470,-p2@HAS2
Hg19::chr8:122653648..122653661,-p3@HAS2
Hg19::chr8:122653664..122653693,-p1@HAS2


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

GO IDGO nameFDR corrected p-value
GO:0050501hyaluronan synthase activity0.00123631225715295
GO:0008194UDP-glycosyltransferase activity0.0284351819145178
GO:0016758transferase activity, transferring hexosyl groups0.0386004160288865
GO:0016757transferase activity, transferring glycosyl groups0.0456405274932297



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue1.19e-1862
striated muscle tissue1.19e-1862
myotome1.19e-1862
muscle tissue2.09e-1864
musculature2.09e-1864
musculature of body2.09e-1864
somite7.12e-1871
presomitic mesoderm7.12e-1871
presumptive segmental plate7.12e-1871
dermomyotome7.12e-1871
trunk paraxial mesoderm7.12e-1871
paraxial mesoderm2.31e-1772
presumptive paraxial mesoderm2.31e-1772
dense mesenchyme tissue7.21e-1773
multilaminar epithelium2.19e-1683
epithelial vesicle2.78e-1578
surface structure5.43e-1399
trunk mesenchyme1.99e-11122
artery2.11e-1142
arterial blood vessel2.11e-1142
arterial system2.11e-1142
systemic artery2.33e-1033
systemic arterial system2.33e-1033
mesenchyme9.67e-09160
entire embryonic mesenchyme9.67e-09160
unilaminar epithelium4.68e-08148
epithelial tube open at both ends7.94e-0859
blood vessel7.94e-0859
blood vasculature7.94e-0859
vascular cord7.94e-0859
integument1.17e-0746
integumental system1.17e-0746
splanchnic layer of lateral plate mesoderm3.50e-0783
smooth muscle tissue3.96e-0715
organism subdivision4.19e-07264
skin of body9.08e-0741
Disease
Ontology termp-valuen
ovarian cancer8.23e-1014


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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