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Coexpression cluster:C519: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004290!6.64e-14!70;UBERON:0000486!1.01e-12!82;UBERON:0000914!1.78e-12!83;UBERON:0002329!1.78e-12!83;UBERON:0003077!1.78e-12!83;UBERON:0003059!1.78e-12!83;UBERON:0007282!1.78e-12!83;UBERON:0009618!1.78e-12!83;UBERON:0007285!1.78e-12!83;UBERON:0002385!3.47e-11!63;UBERON:0001015!3.47e-11!63;UBERON:0000383!3.47e-11!63;UBERON:0001134!7.63e-11!61;UBERON:0002036!7.63e-11!61;UBERON:0003082!7.63e-11!61;UBERON:0000475!7.64e-10!365;UBERON:0005256!2.20e-09!143;UBERON:0002199!3.54e-08!45;UBERON:0002416!3.54e-08!45;UBERON:0002100!3.55e-08!216;UBERON:0000468!1.78e-07!659
|ontology_enrichment_uberon=UBERON:0004290!6.64e-14!70;UBERON:0000486!1.01e-12!82;UBERON:0000914!1.78e-12!83;UBERON:0002329!1.78e-12!83;UBERON:0003077!1.78e-12!83;UBERON:0003059!1.78e-12!83;UBERON:0007282!1.78e-12!83;UBERON:0009618!1.78e-12!83;UBERON:0007285!1.78e-12!83;UBERON:0002385!3.47e-11!63;UBERON:0001015!3.47e-11!63;UBERON:0000383!3.47e-11!63;UBERON:0001134!7.63e-11!61;UBERON:0002036!7.63e-11!61;UBERON:0003082!7.63e-11!61;UBERON:0000475!7.64e-10!365;UBERON:0005256!2.20e-09!143;UBERON:0002199!3.54e-08!45;UBERON:0002416!3.54e-08!45;UBERON:0002100!3.55e-08!216;UBERON:0000468!1.78e-07!659
|tf_chipseq_enrich=ZNF263#10127;7:3.19738285883749:0.00368052163702278:0.0185713595153649
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}}
}}

Revision as of 12:33, 5 September 2012


Full id: C519_Preadipocyte_Ewing_Myoblast_spindle_Fibroblast_Adipocyte_Osteoblast



Phase1 CAGE Peaks

Hg19::chr6:35181725..35181742,+p3@SCUBE3
Hg19::chr6:35181783..35181815,+p2@SCUBE3
Hg19::chr6:35181816..35181850,+p1@SCUBE3
Hg19::chr6:35181866..35181878,+p7@SCUBE3
Hg19::chr6:35181935..35181948,+p4@SCUBE3
Hg19::chr6:35181964..35181980,+p5@SCUBE3
Hg19::chr6:35182176..35182190,+p6@SCUBE3
Hg19::chr6:35200689..35200695,+p9@SCUBE3
Hg19::chr6:35211380..35211391,+p@chr6:35211380..35211391
+
Hg19::chr6:35214004..35214032,+p@chr6:35214004..35214032
+
Hg19::chr6:35216360..35216374,+p10@SCUBE3
Hg19::chr6:35217101..35217114,+p@chr6:35217101..35217114
+
Hg19::chr6:35218080..35218089,+p@chr6:35218080..35218089
+
Hg19::chr6:35218158..35218175,+p@chr6:35218158..35218175
+
Hg19::chr6:35218350..35218364,+p2@AK123742
Hg19::chr6:35218435..35218446,+p4@AK123742
Hg19::chr6:35218509..35218513,+p1@AK123742
Hg19::chr6:35219318..35219336,+p3@AK123742


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:0048196middle lamella-containing extracellular matrix0.000183975038266808
GO:0009505cellulose and pectin-containing cell wall0.000183975038266808
GO:0048222glycoprotein network0.000183975038266808
GO:0009530primary cell wall0.000183975038266808
GO:0005618cell wall0.000294360061226893
GO:0044462external encapsulating structure part0.000490600102044821
GO:0030312external encapsulating structure0.000630771559771913
GO:0051291protein heterooligomerization0.000735900153067232
GO:0051260protein homooligomerization0.00335243403063961
GO:0051259protein oligomerization0.00456258094901684
GO:0044420extracellular matrix part0.00876390182289157
GO:0009986cell surface0.00907610188782919
GO:0006461protein complex assembly0.0192466193879122
GO:0065003macromolecular complex assembly0.0397386082656305
GO:0022607cellular component assembly0.0398857882962439



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
non-terminally differentiated cell3.03e-33180
fibroblast7.32e-1475
muscle precursor cell6.13e-1157
myoblast6.13e-1157
multi-potent skeletal muscle stem cell6.13e-1157
contractile cell1.46e-1059
muscle cell9.46e-1054
electrically responsive cell1.36e-0960
electrically active cell1.36e-0960
preadipocyte2.78e-0912
skin fibroblast1.66e-0823
stromal cell3.35e-0827
Uber Anatomy
Ontology termp-valuen
dermomyotome6.64e-1470
multilaminar epithelium1.01e-1282
somite1.78e-1283
paraxial mesoderm1.78e-1283
presomitic mesoderm1.78e-1283
presumptive segmental plate1.78e-1283
trunk paraxial mesoderm1.78e-1283
presumptive paraxial mesoderm1.78e-1283
muscle tissue3.47e-1163
musculature3.47e-1163
musculature of body3.47e-1163
skeletal muscle tissue7.63e-1161
striated muscle tissue7.63e-1161
myotome7.63e-1161
organism subdivision7.64e-10365
trunk mesenchyme2.20e-09143
integument3.54e-0845
integumental system3.54e-0845
trunk3.55e-08216
multi-cellular organism1.78e-07659


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)

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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
ZNF263#1012773.197382858837490.003680521637022780.0185713595153649



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.