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Coexpression cluster:C3970: Difference between revisions

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|full_id=C3970_Smooth_Fibroblast_basal_Mesothelial_mesenchymal_leiomyoma_Aortic
|full_id=C3970_Smooth_Fibroblast_basal_Mesothelial_mesenchymal_leiomyoma_Aortic
|id=C3970
|id=C3970
|ontology_enrichment_celltype=CL:0000055!4.34e-44!180;CL:0000222!2.53e-27!119;CL:0000680!2.32e-23!57;CL:0000056!2.32e-23!57;CL:0000355!2.32e-23!57;CL:0000220!6.56e-23!246;CL:0000183!7.35e-23!59;CL:0002321!2.46e-22!248;CL:0000187!2.81e-22!54;CL:0002371!4.27e-21!591;CL:0000192!3.26e-20!42;CL:0000514!3.26e-20!42;CL:0000144!4.65e-20!625;CL:0000393!2.25e-19!60;CL:0000211!2.25e-19!60;CL:0000057!1.80e-18!75;CL:0000359!6.87e-18!32;CL:0000548!9.52e-16!679;CL:0000004!9.52e-16!679;CL:0000255!9.52e-16!679;CL:0000012!1.62e-15!682;CL:0000003!3.01e-12!722;CL:0002620!2.64e-09!23;CL:0002139!1.57e-07!24;CL:0002539!2.08e-07!10;CL:0000115!5.13e-07!35;CL:0000071!9.40e-07!18;CL:0002546!9.40e-07!18
|ontology_enrichment_celltype=CL:0000222!1.84e-26!121;CL:0000055!1.30e-23!106;CL:0000680!4.41e-23!58;CL:0000056!4.41e-23!58;CL:0000355!4.41e-23!58;CL:0000183!2.08e-22!59;CL:0002321!2.80e-22!250;CL:0002371!5.93e-22!588;CL:0000187!6.33e-22!55;CL:0000192!4.79e-20!43;CL:0000514!4.79e-20!43;CL:0000057!6.50e-20!76;CL:0000393!5.19e-19!61;CL:0000211!5.19e-19!61;CL:0000359!2.42e-17!32;CL:0000548!3.36e-15!679;CL:0000255!3.36e-15!679;CL:0000003!7.38e-12!722;CL:0002620!1.52e-09!23;CL:0002139!3.83e-07!24;CL:0000048!4.08e-07!427;CL:0002539!5.93e-07!10;CL:0000115!8.12e-07!36
|ontology_enrichment_disease=DOID:2394!1.28e-07!14
|ontology_enrichment_disease=DOID:2394!1.59e-07!14
|ontology_enrichment_uberon=UBERON:0000914!1.41e-24!83;UBERON:0002329!1.41e-24!83;UBERON:0003077!1.41e-24!83;UBERON:0003059!1.41e-24!83;UBERON:0007282!1.41e-24!83;UBERON:0009618!1.41e-24!83;UBERON:0007285!1.41e-24!83;UBERON:0002049!2.40e-24!79;UBERON:0007798!2.40e-24!79;UBERON:0004290!8.32e-23!70;UBERON:0000486!1.03e-22!82;UBERON:0004535!2.32e-22!110;UBERON:0001637!2.34e-22!42;UBERON:0003509!2.34e-22!42;UBERON:0004572!2.34e-22!42;UBERON:0000055!4.69e-22!69;UBERON:0001981!5.09e-21!60;UBERON:0007500!5.09e-21!60;UBERON:0004537!5.09e-21!60;UBERON:0006965!5.09e-21!60;UBERON:0001009!9.55e-21!113;UBERON:0001134!6.67e-20!61;UBERON:0002036!6.67e-20!61;UBERON:0003082!6.67e-20!61;UBERON:0004872!8.70e-20!84;UBERON:0005256!1.68e-19!143;UBERON:0002385!3.12e-19!63;UBERON:0001015!3.12e-19!63;UBERON:0000383!3.12e-19!63;UBERON:0003914!4.77e-18!118;UBERON:0004573!1.17e-17!33;UBERON:0004571!1.17e-17!33;UBERON:0000490!2.84e-17!138;UBERON:0002100!4.41e-14!216;UBERON:0000475!6.63e-14!365;UBERON:0000119!1.45e-13!312;UBERON:0000483!5.23e-13!309;UBERON:0000947!3.95e-10!21;UBERON:0010191!3.95e-10!21;UBERON:0000467!4.30e-09!625;UBERON:0000480!6.90e-09!626;UBERON:0000468!7.66e-09!659;UBERON:0003102!1.04e-08!95;UBERON:0002199!3.39e-08!45;UBERON:0002416!3.39e-08!45;UBERON:0004111!8.58e-08!241;UBERON:0004237!2.08e-07!10;UBERON:0004695!2.08e-07!10;UBERON:0002111!2.08e-07!10;UBERON:0004178!2.08e-07!10;UBERON:0000487!2.34e-07!22;UBERON:0000477!3.73e-07!286;UBERON:0000481!3.79e-07!347;UBERON:0000025!6.50e-07!194;UBERON:0003104!6.97e-07!238;UBERON:0009142!6.97e-07!238;UBERON:0002097!7.76e-07!40;UBERON:0001986!9.40e-07!18;UBERON:0004638!9.40e-07!18;UBERON:0004852!9.40e-07!18
|ontology_enrichment_uberon=UBERON:0007503!3.06e-24!78;UBERON:0002049!1.31e-23!78;UBERON:0007798!1.31e-23!78;UBERON:0000486!5.90e-23!83;UBERON:0002329!7.78e-23!71;UBERON:0003059!7.78e-23!71;UBERON:0007282!7.78e-23!71;UBERON:0004290!7.78e-23!71;UBERON:0009618!7.78e-23!71;UBERON:0007524!1.76e-22!73;UBERON:0003077!2.09e-22!72;UBERON:0007285!2.09e-22!72;UBERON:0001637!1.00e-21!42;UBERON:0003509!1.00e-21!42;UBERON:0004572!1.00e-21!42;UBERON:0004535!2.27e-21!109;UBERON:0000055!5.77e-21!68;UBERON:0000490!6.86e-20!148;UBERON:0001134!7.83e-20!62;UBERON:0002036!7.83e-20!62;UBERON:0003082!7.83e-20!62;UBERON:0007500!9.46e-20!59;UBERON:0001981!9.46e-20!59;UBERON:0004537!9.46e-20!59;UBERON:0006965!9.46e-20!59;UBERON:0001009!1.55e-19!112;UBERON:0002385!4.67e-19!64;UBERON:0001015!4.67e-19!64;UBERON:0000383!4.67e-19!64;UBERON:0004872!9.68e-19!83;UBERON:0004573!4.15e-17!33;UBERON:0004571!4.15e-17!33;UBERON:0003914!1.08e-16!117;UBERON:0005256!6.72e-16!122;UBERON:0000119!1.89e-14!309;UBERON:0000483!9.29e-14!306;UBERON:0003104!6.06e-13!160;UBERON:0009142!6.06e-13!160;UBERON:0000475!8.67e-13!264;UBERON:0002100!2.82e-11!199;UBERON:0000947!1.25e-09!21;UBERON:0010191!1.25e-09!21;UBERON:0000467!1.33e-09!624;UBERON:0000480!2.13e-09!625;UBERON:0003102!4.90e-09!99;UBERON:0000468!7.48e-09!656;UBERON:0000926!1.17e-08!315;UBERON:0004120!1.17e-08!315;UBERON:0006603!1.17e-08!315;UBERON:0002199!2.64e-08!46;UBERON:0002416!2.64e-08!46;UBERON:0004111!2.56e-07!240;UBERON:0002097!4.25e-07!41;UBERON:0000487!4.41e-07!22;UBERON:0004237!5.93e-07!10;UBERON:0004695!5.93e-07!10;UBERON:0002111!5.93e-07!10;UBERON:0004178!5.93e-07!10
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115288594200001!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320928966580284!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898248223536612!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000371378347095231!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444561689954406!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000680909380201387!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156916015024528!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000301962574142921
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115288594200001!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320928966580284!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898248223536612!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000371378347095231!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444561689954406!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000680909380201387!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156916015024528!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000301962574142921
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}}
}}

Revision as of 15:33, 19 October 2012


Full id: C3970_Smooth_Fibroblast_basal_Mesothelial_mesenchymal_leiomyoma_Aortic



Phase1 CAGE Peaks

Hg19::chr1:32264166..32264245,-p2@SPOCD1
Hg19::chr1:32264250..32264354,-p1@SPOCD1
Hg19::chr1:32264356..32264380,-p3@SPOCD1


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle3.06e-2478
vasculature1.31e-2378
vascular system1.31e-2378
multilaminar epithelium5.90e-2383
somite7.78e-2371
presomitic mesoderm7.78e-2371
presumptive segmental plate7.78e-2371
dermomyotome7.78e-2371
trunk paraxial mesoderm7.78e-2371
dense mesenchyme tissue1.76e-2273
paraxial mesoderm2.09e-2272
presumptive paraxial mesoderm2.09e-2272
artery1.00e-2142
arterial blood vessel1.00e-2142
arterial system1.00e-2142
cardiovascular system2.27e-21109
vessel5.77e-2168
unilaminar epithelium6.86e-20148
skeletal muscle tissue7.83e-2062
striated muscle tissue7.83e-2062
myotome7.83e-2062
epithelial tube open at both ends9.46e-2059
blood vessel9.46e-2059
blood vasculature9.46e-2059
vascular cord9.46e-2059
circulatory system1.55e-19112
muscle tissue4.67e-1964
musculature4.67e-1964
musculature of body4.67e-1964
splanchnic layer of lateral plate mesoderm9.68e-1983
systemic artery4.15e-1733
systemic arterial system4.15e-1733
epithelial tube1.08e-16117
trunk mesenchyme6.72e-16122
cell layer1.89e-14309
epithelium9.29e-14306
mesenchyme6.06e-13160
entire embryonic mesenchyme6.06e-13160
organism subdivision8.67e-13264
trunk2.82e-11199
aorta1.25e-0921
aortic system1.25e-0921
anatomical system1.33e-09624
anatomical group2.13e-09625
surface structure4.90e-0999
multi-cellular organism7.48e-09656
mesoderm1.17e-08315
mesoderm-derived structure1.17e-08315
presumptive mesoderm1.17e-08315
integument2.64e-0846
integumental system2.64e-0846
anatomical conduit2.56e-07240
skin of body4.25e-0741
simple squamous epithelium4.41e-0722
blood vessel smooth muscle5.93e-0710
arterial system smooth muscle5.93e-0710
artery smooth muscle tissue5.93e-0710
aorta smooth muscle tissue5.93e-0710
Disease
Ontology termp-valuen
ovarian cancer1.59e-0714


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
CEBPB#105137.971147625824820.001974187055288560.0115288594200001
EGR1#195834.988179094810140.008056488137383440.0320928966580284
FOS#235338.99795530889440.001372499272417130.00898248223536612
FOSL1#8061339.7135797163731.59554825631833e-050.000371378347095231
JUN#3725312.51282919233630.0005103313992726250.00444561689954406
JUNB#3726330.61063265982113.4847716247536e-050.000680909380201387
JUND#372736.994663941871030.002921845042734990.0156916015024528
SMARCC1#6599343.66335931963151.20046018043203e-050.000301962574142921



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3970&oldid=2250250"