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Coexpression cluster:C1528: Difference between revisions

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|full_id=C1528_Mesenchymal_Pericytes_mesodermal_Adipocyte_Fibroblast_Multipotent_Hair
|full_id=C1528_Mesenchymal_Pericytes_mesodermal_Adipocyte_Fibroblast_Multipotent_Hair
|id=C1528
|id=C1528
|ontology_enrichment_celltype=CL:0000055!5.06e-28!180;CL:0000057!4.64e-22!75;CL:0002620!2.44e-09!23;CL:0000183!8.90e-09!59;CL:0000187!6.29e-08!54;CL:0000136!7.42e-08!15;CL:0000680!8.66e-08!57;CL:0000056!8.66e-08!57;CL:0000355!8.66e-08!57;CL:0000393!4.83e-07!60;CL:0000211!4.83e-07!60;CL:0002334!5.88e-07!12
|ontology_enrichment_celltype=CL:0000057!9.78e-25!76;CL:0000183!1.12e-10!59;CL:0002620!4.82e-10!23;CL:0000187!1.98e-09!55;CL:0000680!2.72e-09!58;CL:0000056!2.72e-09!58;CL:0000355!2.72e-09!58;CL:0000055!8.37e-09!106;CL:0000136!3.24e-08!15;CL:0000393!1.16e-07!61;CL:0000211!1.16e-07!61;CL:0002334!3.16e-07!12
|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:0007524!1.56e-13!73;UBERON:0010314!1.86e-13!132;UBERON:0000481!2.87e-13!342;UBERON:0003077!4.91e-13!72;UBERON:0007285!4.91e-13!72;UBERON:0002329!4.94e-13!71;UBERON:0003059!4.94e-13!71;UBERON:0007282!4.94e-13!71;UBERON:0004290!4.94e-13!71;UBERON:0009618!4.94e-13!71;UBERON:0007503!1.91e-12!78;UBERON:0007023!1.47e-11!114;UBERON:0002385!1.02e-10!64;UBERON:0001015!1.02e-10!64;UBERON:0000383!1.02e-10!64;UBERON:0003104!1.32e-10!160;UBERON:0009142!1.32e-10!160;UBERON:0001134!1.92e-10!62;UBERON:0002036!1.92e-10!62;UBERON:0003082!1.92e-10!62;UBERON:0002199!1.06e-09!46;UBERON:0002416!1.06e-09!46;UBERON:0000479!1.78e-09!773;UBERON:0003102!2.34e-09!99;UBERON:0000486!4.71e-09!83;UBERON:0005256!4.79e-09!122;UBERON:0001013!9.37e-09!14;UBERON:0000468!3.84e-08!656;UBERON:0000475!4.12e-08!264;UBERON:0002097!1.15e-07!41;UBERON:0003075!1.45e-07!82;UBERON:0007284!1.45e-07!82;UBERON:0004121!1.77e-07!171;UBERON:0000924!1.77e-07!171;UBERON:0006601!1.77e-07!171;UBERON:0002346!3.79e-07!86
|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
|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 11:24, 19 October 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
fibroblast9.78e-2576
contractile cell1.12e-1059
skin fibroblast4.82e-1023
muscle cell1.98e-0955
muscle precursor cell2.72e-0958
myoblast2.72e-0958
multi-potent skeletal muscle stem cell2.72e-0958
non-terminally differentiated cell8.37e-09106
fat cell3.24e-0815
electrically responsive cell1.16e-0761
electrically active cell1.16e-0761
preadipocyte3.16e-0712
Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue1.56e-1373
structure with developmental contribution from neural crest1.86e-13132
multi-tissue structure2.87e-13342
paraxial mesoderm4.91e-1372
presumptive paraxial mesoderm4.91e-1372
somite4.94e-1371
presomitic mesoderm4.94e-1371
presumptive segmental plate4.94e-1371
dermomyotome4.94e-1371
trunk paraxial mesoderm4.94e-1371
epithelial vesicle1.91e-1278
adult organism1.47e-11114
muscle tissue1.02e-1064
musculature1.02e-1064
musculature of body1.02e-1064
mesenchyme1.32e-10160
entire embryonic mesenchyme1.32e-10160
skeletal muscle tissue1.92e-1062
striated muscle tissue1.92e-1062
myotome1.92e-1062
integument1.06e-0946
integumental system1.06e-0946
tissue1.78e-09773
surface structure2.34e-0999
multilaminar epithelium4.71e-0983
trunk mesenchyme4.79e-09122
adipose tissue9.37e-0914
multi-cellular organism3.84e-08656
organism subdivision4.12e-08264
skin of body1.15e-0741
neural plate1.45e-0782
presumptive neural plate1.45e-0782
ectoderm-derived structure1.77e-07171
ectoderm1.77e-07171
presumptive ectoderm1.77e-07171
neurectoderm3.79e-0786


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.