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Coexpression cluster:C1000: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007503!5.82e-16!78;UBERON:0007524!6.58e-16!73;UBERON:0002329!8.86e-16!71;UBERON:0003059!8.86e-16!71;UBERON:0007282!8.86e-16!71;UBERON:0004290!8.86e-16!71;UBERON:0009618!8.86e-16!71;UBERON:0003077!2.73e-15!72;UBERON:0007285!2.73e-15!72;UBERON:0002385!2.39e-13!64;UBERON:0001015!2.39e-13!64;UBERON:0000383!2.39e-13!64;UBERON:0001134!4.76e-13!62;UBERON:0002036!4.76e-13!62;UBERON:0003082!4.76e-13!62;UBERON:0000486!1.19e-12!83;UBERON:0005256!2.66e-12!122;UBERON:0003104!6.83e-12!160;UBERON:0009142!6.83e-12!160;UBERON:0004923!1.27e-11!66;UBERON:0000475!6.08e-10!264;UBERON:0002199!2.30e-09!46;UBERON:0002416!2.30e-09!46;UBERON:0003102!6.34e-09!99;UBERON:0000926!1.04e-08!315;UBERON:0004120!1.04e-08!315;UBERON:0006603!1.04e-08!315;UBERON:0002100!1.71e-08!199;UBERON:0002097!6.29e-08!41;UBERON:0005631!1.82e-07!14;UBERON:0000158!1.82e-07!14;UBERON:0002384!2.94e-07!371;UBERON:0004872!3.46e-07!83;UBERON:0001013!4.26e-07!14;UBERON:0000479!7.35e-07!773
|ontology_enrichment_uberon=UBERON:0007503!5.82e-16!78;UBERON:0007524!6.58e-16!73;UBERON:0002329!8.86e-16!71;UBERON:0003059!8.86e-16!71;UBERON:0007282!8.86e-16!71;UBERON:0004290!8.86e-16!71;UBERON:0009618!8.86e-16!71;UBERON:0003077!2.73e-15!72;UBERON:0007285!2.73e-15!72;UBERON:0002385!2.39e-13!64;UBERON:0001015!2.39e-13!64;UBERON:0000383!2.39e-13!64;UBERON:0001134!4.76e-13!62;UBERON:0002036!4.76e-13!62;UBERON:0003082!4.76e-13!62;UBERON:0000486!1.19e-12!83;UBERON:0005256!2.66e-12!122;UBERON:0003104!6.83e-12!160;UBERON:0009142!6.83e-12!160;UBERON:0004923!1.27e-11!66;UBERON:0000475!6.08e-10!264;UBERON:0002199!2.30e-09!46;UBERON:0002416!2.30e-09!46;UBERON:0003102!6.34e-09!99;UBERON:0000926!1.04e-08!315;UBERON:0004120!1.04e-08!315;UBERON:0006603!1.04e-08!315;UBERON:0002100!1.71e-08!199;UBERON:0002097!6.29e-08!41;UBERON:0005631!1.82e-07!14;UBERON:0000158!1.82e-07!14;UBERON:0002384!2.94e-07!371;UBERON:0004872!3.46e-07!83;UBERON:0001013!4.26e-07!14;UBERON:0000479!7.35e-07!773
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}}
}}

Revision as of 14:37, 26 November 2012


Full id: C1000_Osteoblast_Preadipocyte_Hair_Adipocyte_tenocyte_Mesenchymal_leiomyoma



Phase1 CAGE Peaks

Hg19::chr11:65638757..65638772,-p4@EFEMP2
Hg19::chr16:4431039..4431055,+p3@VASN
Hg19::chr1:1288794..1288843,-p@chr1:1288794..1288843
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Hg19::chr1:1289264..1289283,-p@chr1:1289264..1289283
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Hg19::chr1:1289610..1289617,-p6@MXRA8
Hg19::chr1:1289800..1289816,-p11@MXRA8
Hg19::chr1:1290090..1290114,-p4@MXRA8
Hg19::chr3:124560257..124560266,-p@chr3:124560257..124560266
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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:0005604basement membrane0.0432155128362482
GO:0007596blood coagulation0.0432155128362482
GO:0050817coagulation0.0432155128362482
GO:0007599hemostasis0.0432155128362482
GO:0005201extracellular matrix structural constituent0.0432155128362482
GO:0050878regulation of body fluid levels0.0432155128362482
GO:0042060wound healing0.0432155128362482
GO:0044420extracellular matrix part0.0432155128362482



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
epithelial vesicle5.82e-1678
dense mesenchyme tissue6.58e-1673
somite8.86e-1671
presomitic mesoderm8.86e-1671
presumptive segmental plate8.86e-1671
dermomyotome8.86e-1671
trunk paraxial mesoderm8.86e-1671
paraxial mesoderm2.73e-1572
presumptive paraxial mesoderm2.73e-1572
muscle tissue2.39e-1364
musculature2.39e-1364
musculature of body2.39e-1364
skeletal muscle tissue4.76e-1362
striated muscle tissue4.76e-1362
myotome4.76e-1362
multilaminar epithelium1.19e-1283
trunk mesenchyme2.66e-12122
mesenchyme6.83e-12160
entire embryonic mesenchyme6.83e-12160
organ component layer1.27e-1166
organism subdivision6.08e-10264
integument2.30e-0946
integumental system2.30e-0946
surface structure6.34e-0999
mesoderm1.04e-08315
mesoderm-derived structure1.04e-08315
presumptive mesoderm1.04e-08315
trunk1.71e-08199
skin of body6.29e-0841
extraembryonic membrane1.82e-0714
membranous layer1.82e-0714
connective tissue2.94e-07371
splanchnic layer of lateral plate mesoderm3.46e-0783
adipose tissue4.26e-0714
tissue7.35e-07773


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.