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Coexpression cluster:C1528: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!7.68e-19!365;UBERON:0000914!1.26e-13!83;UBERON:0002329!1.26e-13!83;UBERON:0003077!1.26e-13!83;UBERON:0003059!1.26e-13!83;UBERON:0007282!1.26e-13!83;UBERON:0009618!1.26e-13!83;UBERON:0007285!1.26e-13!83;UBERON:0007023!6.96e-13!115;UBERON:0004290!3.07e-11!70;UBERON:0000481!8.63e-11!347;UBERON:0005256!1.24e-09!143;UBERON:0002385!3.48e-09!63;UBERON:0001015!3.48e-09!63;UBERON:0000383!3.48e-09!63;UBERON:0001134!6.75e-09!61;UBERON:0002036!6.75e-09!61;UBERON:0003082!6.75e-09!61;UBERON:0001013!1.01e-08!14;UBERON:0000033!1.11e-08!123;UBERON:0000153!1.28e-08!129;UBERON:0007811!1.28e-08!129;UBERON:0000486!7.66e-08!82;UBERON:0002199!8.23e-08!45;UBERON:0002416!8.23e-08!45;UBERON:0000468!1.47e-07!659;UBERON:0005743!1.50e-07!86;UBERON:0003075!1.51e-07!86;UBERON:0007284!1.51e-07!86;UBERON:0003102!1.51e-07!95;UBERON:0004121!1.58e-07!169;UBERON:0000924!2.16e-07!173;UBERON:0006601!2.16e-07!173;UBERON:0002346!2.85e-07!90;UBERON:0000073!3.27e-07!94;UBERON:0001016!3.27e-07!94;UBERON:0001017!7.87e-07!82;UBERON:0002100!8.97e-07!216
|ontology_enrichment_uberon=UBERON:0000475!7.68e-19!365;UBERON:0000914!1.26e-13!83;UBERON:0002329!1.26e-13!83;UBERON:0003077!1.26e-13!83;UBERON:0003059!1.26e-13!83;UBERON:0007282!1.26e-13!83;UBERON:0009618!1.26e-13!83;UBERON:0007285!1.26e-13!83;UBERON:0007023!6.96e-13!115;UBERON:0004290!3.07e-11!70;UBERON:0000481!8.63e-11!347;UBERON:0005256!1.24e-09!143;UBERON:0002385!3.48e-09!63;UBERON:0001015!3.48e-09!63;UBERON:0000383!3.48e-09!63;UBERON:0001134!6.75e-09!61;UBERON:0002036!6.75e-09!61;UBERON:0003082!6.75e-09!61;UBERON:0001013!1.01e-08!14;UBERON:0000033!1.11e-08!123;UBERON:0000153!1.28e-08!129;UBERON:0007811!1.28e-08!129;UBERON:0000486!7.66e-08!82;UBERON:0002199!8.23e-08!45;UBERON:0002416!8.23e-08!45;UBERON:0000468!1.47e-07!659;UBERON:0005743!1.50e-07!86;UBERON:0003075!1.51e-07!86;UBERON:0007284!1.51e-07!86;UBERON:0003102!1.51e-07!95;UBERON:0004121!1.58e-07!169;UBERON:0000924!2.16e-07!173;UBERON:0006601!2.16e-07!173;UBERON:0002346!2.85e-07!90;UBERON:0000073!3.27e-07!94;UBERON:0001016!3.27e-07!94;UBERON:0001017!7.87e-07!82;UBERON:0002100!8.97e-07!216
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000756132739886017!EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000269913653049002!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380717730044966!RAD21#5885;6:10.3550338954563:8.10515055094479e-07:3.54478148404574e-05!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.0057373957034289!YY1#7528;6:4.91117074985386:7.12445972864136e-05:0.00112431467150132
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}}
}}

Revision as of 13:51, 5 September 2012


Full id: C1528_Mesenchymal_Pericytes_mesodermal_Adipocyte_Fibroblast_Multipotent_Hair



Phase1 CAGE Peaks

Hg19::chr5:149535244..149535282,-p4@PDGFRB
Hg19::chr5:149535298..149535305,-p6@PDGFRB
Hg19::chr5:149535335..149535359,-p3@PDGFRB
Hg19::chr5:149535378..149535385,-p5@PDGFRB
Hg19::chr5:149535392..149535417,-p1@PDGFRB
Hg19::chr5:149535421..149535441,-p2@PDGFRB


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
non-terminally differentiated cell5.06e-28180
fibroblast4.64e-2275
skin fibroblast2.44e-0923
contractile cell8.90e-0959
muscle cell6.29e-0854
fat cell7.42e-0815
muscle precursor cell8.66e-0857
myoblast8.66e-0857
multi-potent skeletal muscle stem cell8.66e-0857
electrically responsive cell4.83e-0760
electrically active cell4.83e-0760
preadipocyte5.88e-0712
Uber Anatomy
Ontology termp-valuen
organism subdivision7.68e-19365
somite1.26e-1383
paraxial mesoderm1.26e-1383
presomitic mesoderm1.26e-1383
presumptive segmental plate1.26e-1383
trunk paraxial mesoderm1.26e-1383
presumptive paraxial mesoderm1.26e-1383
adult organism6.96e-13115
dermomyotome3.07e-1170
multi-tissue structure8.63e-11347
trunk mesenchyme1.24e-09143
muscle tissue3.48e-0963
musculature3.48e-0963
musculature of body3.48e-0963
skeletal muscle tissue6.75e-0961
striated muscle tissue6.75e-0961
myotome6.75e-0961
adipose tissue1.01e-0814
head1.11e-08123
anterior region of body1.28e-08129
craniocervical region1.28e-08129
multilaminar epithelium7.66e-0882
integument8.23e-0845
integumental system8.23e-0845
multi-cellular organism1.47e-07659
neural plate1.51e-0786
presumptive neural plate1.51e-0786
surface structure1.51e-0795
ectoderm-derived structure1.58e-07169
ectoderm2.16e-07173
presumptive ectoderm2.16e-07173
neurectoderm2.85e-0790
regional part of nervous system3.27e-0794
nervous system3.27e-0794
central nervous system7.87e-0782
trunk8.97e-07216


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
CTCF#1066465.360256373075034.21437267579784e-050.000756132739886017
EP300#203366.77394172622321.03454107484288e-050.000269913653049002
POLR2A#543062.147453176558070.01019570676818780.0380717730044966
RAD21#5885610.35503389545638.10515055094479e-073.54478148404574e-05
TAF1#687263.343046285745290.0007162474284635620.0057373957034289
YY1#752864.911170749853867.12445972864136e-050.00112431467150132



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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