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Coexpression cluster:C2373: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2373_Mesenchymal_Renal_leiomyoblastoma_Hepatic_Pericytes_Fibroblast_Smooth
|full_id=C2373_Mesenchymal_Renal_leiomyoblastoma_Hepatic_Pericytes_Fibroblast_Smooth
|id=C2373
|id=C2373

Revision as of 15:05, 12 September 2012


Full id: C2373_Mesenchymal_Renal_leiomyoblastoma_Hepatic_Pericytes_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr16:447209..447225,+p2@NME4
Hg19::chr16:447226..447242,+p3@NME4
Hg19::chr16:447255..447266,+p4@NME4
Hg19::chr16:447267..447272,+p6@NME4


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
trunk mesenchyme2.90e-22143
trunk8.10e-19216
somite1.13e-1883
paraxial mesoderm1.13e-1883
presomitic mesoderm1.13e-1883
presumptive segmental plate1.13e-1883
trunk paraxial mesoderm1.13e-1883
presumptive paraxial mesoderm1.13e-1883
epithelial tube4.27e-18118
dermomyotome5.35e-1870
vasculature6.84e-1879
vascular system6.84e-1879
multilaminar epithelium1.07e-1782
skeletal muscle tissue3.04e-1761
striated muscle tissue3.04e-1761
myotome3.04e-1761
muscle tissue3.15e-1763
musculature3.15e-1763
musculature of body3.15e-1763
unilaminar epithelium9.58e-17138
splanchnic layer of lateral plate mesoderm2.99e-1684
blood vessel1.02e-1460
epithelial tube open at both ends1.02e-1460
blood vasculature1.02e-1460
vascular cord1.02e-1460
vessel1.12e-1469
artery1.16e-1342
arterial blood vessel1.16e-1342
arterial system1.16e-1342
cardiovascular system1.37e-12110
circulatory system2.72e-12113
mesenchyme1.61e-11238
entire embryonic mesenchyme1.61e-11238
organism subdivision4.12e-11365
cell layer1.99e-10312
systemic artery2.55e-1033
systemic arterial system2.55e-1033
epithelium3.36e-10309
subdivision of trunk1.37e-08113
multi-tissue structure3.23e-07347


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
CCNT2#90546.336201576962630.0006203100587215640.00511766823784039
CTCFL#140690419.74647435897446.5732084880439e-060.000192728613498825
E2F1#186944.907389214879320.001724022357361790.0106428165847327
E2F6#187645.017155731697390.00157802193473060.00996354711573236
EGR1#195844.988179094810140.001615011500076050.0101382572613117
ETS1#211349.728760922202340.0001115955317418140.00154431240752395
HEY1#2346244.040111043105710.00375304636917980.0185844393224963
HMGN3#932448.178547723350590.0002234570284440470.00247982452381977
JUND#372746.994663941871030.000417684217818580.00391373784539339
PAX5#507946.669565531177830.0005052774169483260.0044356281540444
SIN3A#2594245.408884726815140.001168172384885160.00795583669416504
TAF1#687243.343046285745290.008005664898701650.0321863046678024
YY1#752844.911170749853860.00171871838055440.0106731614310097
ZBTB7A#5134147.35190930787590.000342223540015990.00346265106527126



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.