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Coexpression cluster:C2779: Difference between revisions

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|full_id=C2779_Adipocyte_mature_adipose_Preadipocyte_Fibroblast_Mesenchymal_Hair
|full_id=C2779_Adipocyte_mature_adipose_Preadipocyte_Fibroblast_Mesenchymal_Hair
|id=C2779
|id=C2779
|ontology_enrichment_celltype=CL:0000222!2.63e-15!119;CL:0000055!6.64e-14!180;CL:0000057!2.60e-12!75;CL:0002139!2.39e-11!24;CL:0000680!4.23e-11!57;CL:0000056!4.23e-11!57;CL:0000355!4.23e-11!57;CL:0000136!8.06e-11!15;CL:0000187!3.11e-10!54;CL:0000183!5.42e-10!59;CL:0000115!3.24e-09!35;CL:0000071!1.30e-08!18;CL:0002546!1.30e-08!18;CL:0002078!1.94e-08!44;CL:0000192!7.16e-08!42;CL:0000514!7.16e-08!42;CL:0000393!2.82e-07!60;CL:0000211!2.82e-07!60;CL:0002334!9.39e-07!12
|ontology_enrichment_celltype=CL:0000222!3.58e-15!121;CL:0002139!1.98e-13!24;CL:0000136!1.35e-11!15;CL:0000115!6.74e-11!36;CL:0000680!8.48e-11!58;CL:0000056!8.48e-11!58;CL:0000355!8.48e-11!58;CL:0000071!6.57e-10!18;CL:0002546!6.57e-10!18;CL:0000057!7.19e-10!76;CL:0000187!8.12e-10!55;CL:0002078!1.79e-09!45;CL:0000183!3.44e-08!59;CL:0000192!4.70e-08!43;CL:0000514!4.70e-08!43;CL:0002334!8.75e-08!12;CL:0000393!1.76e-07!61;CL:0000211!1.76e-07!61;CL:1000413!6.83e-07!9;CL:0000213!8.39e-07!58;CL:0000215!8.39e-07!58
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!5.78e-19!84;UBERON:0000477!8.19e-19!286;UBERON:0000475!1.63e-18!365;UBERON:0004111!1.85e-18!241;UBERON:0000119!3.27e-18!312;UBERON:0002049!6.46e-18!79;UBERON:0007798!6.46e-18!79;UBERON:0000483!7.55e-18!309;UBERON:0000468!8.47e-17!659;UBERON:0000055!1.28e-16!69;UBERON:0000914!1.81e-16!83;UBERON:0002329!1.81e-16!83;UBERON:0003077!1.81e-16!83;UBERON:0003059!1.81e-16!83;UBERON:0007282!1.81e-16!83;UBERON:0009618!1.81e-16!83;UBERON:0007285!1.81e-16!83;UBERON:0001009!4.70e-15!113;UBERON:0001981!7.74e-15!60;UBERON:0007500!7.74e-15!60;UBERON:0004537!7.74e-15!60;UBERON:0006965!7.74e-15!60;UBERON:0004535!1.16e-14!110;UBERON:0000486!1.19e-14!82;UBERON:0000467!5.43e-14!625;UBERON:0000480!9.41e-14!626;UBERON:0004290!2.21e-13!70;UBERON:0007023!3.01e-13!115;UBERON:0000025!4.81e-13!194;UBERON:0002385!1.32e-12!63;UBERON:0001015!1.32e-12!63;UBERON:0000383!1.32e-12!63;UBERON:0001134!4.10e-12!61;UBERON:0002036!4.10e-12!61;UBERON:0003082!4.10e-12!61;UBERON:0000481!4.85e-12!347;UBERON:0003914!2.87e-11!118;UBERON:0000490!7.60e-11!138;UBERON:0005256!9.85e-11!143;UBERON:0002100!3.41e-10!216;UBERON:0001637!9.78e-10!42;UBERON:0003509!9.78e-10!42;UBERON:0004572!9.78e-10!42;UBERON:0004573!2.24e-09!33;UBERON:0004571!2.24e-09!33;UBERON:0002050!3.16e-09!605;UBERON:0005423!3.16e-09!605;UBERON:0000923!3.34e-09!604;UBERON:0005291!3.34e-09!604;UBERON:0006598!3.34e-09!604;UBERON:0002532!3.34e-09!604;UBERON:0000922!6.70e-09!612;UBERON:0001986!1.30e-08!18;UBERON:0004638!1.30e-08!18;UBERON:0004852!1.30e-08!18;UBERON:0000479!1.24e-07!787;UBERON:0000947!1.68e-07!21;UBERON:0010191!1.68e-07!21;UBERON:0006914!1.89e-07!25;UBERON:0001013!2.22e-07!14;UBERON:0000033!3.17e-07!123;UBERON:0003102!3.46e-07!95;UBERON:0000153!4.85e-07!129;UBERON:0007811!4.85e-07!129;UBERON:0007100!7.06e-07!27;UBERON:0000487!9.07e-07!22
|ontology_enrichment_uberon=UBERON:0004872!9.88e-19!83;UBERON:0000055!6.35e-18!68;UBERON:0002049!1.03e-17!78;UBERON:0007798!1.03e-17!78;UBERON:0007500!1.61e-16!59;UBERON:0001981!1.61e-16!59;UBERON:0004537!1.61e-16!59;UBERON:0006965!1.61e-16!59;UBERON:0001009!7.78e-16!112;UBERON:0004535!3.41e-15!109;UBERON:0000486!5.39e-14!83;UBERON:0000468!1.35e-13!656;UBERON:0002329!8.67e-13!71;UBERON:0003059!8.67e-13!71;UBERON:0007282!8.67e-13!71;UBERON:0004290!8.67e-13!71;UBERON:0009618!8.67e-13!71;UBERON:0002385!9.27e-13!64;UBERON:0001015!9.27e-13!64;UBERON:0000383!9.27e-13!64;UBERON:0007503!1.63e-12!78;UBERON:0007524!2.16e-12!73;UBERON:0003077!2.45e-12!72;UBERON:0007285!2.45e-12!72;UBERON:0001134!3.62e-12!62;UBERON:0002036!3.62e-12!62;UBERON:0003082!3.62e-12!62;UBERON:0004111!4.95e-12!240;UBERON:0003914!9.09e-12!117;UBERON:0000467!1.21e-11!624;UBERON:0000480!1.74e-11!625;UBERON:0000119!2.43e-11!309;UBERON:0004573!3.45e-11!33;UBERON:0004571!3.45e-11!33;UBERON:0000490!4.04e-11!148;UBERON:0000483!4.09e-11!306;UBERON:0001637!7.47e-11!42;UBERON:0003509!7.47e-11!42;UBERON:0004572!7.47e-11!42;UBERON:0004638!6.57e-10!18;UBERON:0001986!6.57e-10!18;UBERON:0004852!6.57e-10!18;UBERON:0000926!1.64e-09!315;UBERON:0004120!1.64e-09!315;UBERON:0006603!1.64e-09!315;UBERON:0000475!3.81e-09!264;UBERON:0000025!8.25e-09!192;UBERON:0000477!9.21e-09!373;UBERON:0000947!9.84e-09!21;UBERON:0010191!9.84e-09!21;UBERON:0005256!1.15e-08!122;UBERON:0002050!2.85e-08!564;UBERON:0000481!4.98e-08!342;UBERON:0007023!5.87e-08!114;UBERON:0000923!1.40e-07!560;UBERON:0010316!1.40e-07!560;UBERON:0005291!1.40e-07!560;UBERON:0006598!1.40e-07!560;UBERON:0010317!1.40e-07!560;UBERON:0002532!1.40e-07!560;UBERON:0004923!1.73e-07!66;UBERON:0006914!2.41e-07!25;UBERON:0002100!2.64e-07!199;UBERON:0003102!3.32e-07!99;UBERON:0003915!6.83e-07!9;UBERON:0004700!6.83e-07!9;UBERON:0001917!6.83e-07!9;UBERON:0000479!7.74e-07!773;UBERON:0000487!8.39e-07!22
|tf_chipseq_enrich=FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195249940925154!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107261210190565!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074466032738673
|tf_chipseq_enrich=FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195249940925154!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107261210190565!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074466032738673
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}}
}}

Revision as of 14:24, 19 October 2012


Full id: C2779_Adipocyte_mature_adipose_Preadipocyte_Fibroblast_Mesenchymal_Hair



Phase1 CAGE Peaks

Hg19::chr4:152148941..152148953,-p3@SH3D19
Hg19::chr4:152148984..152149004,-p4@SH3D19
Hg19::chr4:152149009..152149020,-p7@SH3D19
Hg19::chr4:152149033..152149117,-p1@SH3D19


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>

Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm9.88e-1983
vessel6.35e-1868
vasculature1.03e-1778
vascular system1.03e-1778
epithelial tube open at both ends1.61e-1659
blood vessel1.61e-1659
blood vasculature1.61e-1659
vascular cord1.61e-1659
circulatory system7.78e-16112
cardiovascular system3.41e-15109
multilaminar epithelium5.39e-1483
multi-cellular organism1.35e-13656
somite8.67e-1371
presomitic mesoderm8.67e-1371
presumptive segmental plate8.67e-1371
dermomyotome8.67e-1371
trunk paraxial mesoderm8.67e-1371
muscle tissue9.27e-1364
musculature9.27e-1364
musculature of body9.27e-1364
epithelial vesicle1.63e-1278
dense mesenchyme tissue2.16e-1273
paraxial mesoderm2.45e-1272
presumptive paraxial mesoderm2.45e-1272
skeletal muscle tissue3.62e-1262
striated muscle tissue3.62e-1262
myotome3.62e-1262
anatomical conduit4.95e-12240
epithelial tube9.09e-12117
anatomical system1.21e-11624
anatomical group1.74e-11625
cell layer2.43e-11309
systemic artery3.45e-1133
systemic arterial system3.45e-1133
unilaminar epithelium4.04e-11148
epithelium4.09e-11306
artery7.47e-1142
arterial blood vessel7.47e-1142
arterial system7.47e-1142
blood vessel endothelium6.57e-1018
endothelium6.57e-1018
cardiovascular system endothelium6.57e-1018
mesoderm1.64e-09315
mesoderm-derived structure1.64e-09315
presumptive mesoderm1.64e-09315
organism subdivision3.81e-09264
tube8.25e-09192
anatomical cluster9.21e-09373
aorta9.84e-0921
aortic system9.84e-0921
trunk mesenchyme1.15e-08122
embryonic structure2.85e-08564
multi-tissue structure4.98e-08342
adult organism5.87e-08114
germ layer1.40e-07560
germ layer / neural crest1.40e-07560
embryonic tissue1.40e-07560
presumptive structure1.40e-07560
germ layer / neural crest derived structure1.40e-07560
epiblast (generic)1.40e-07560
organ component layer1.73e-0766
squamous epithelium2.41e-0725
trunk2.64e-07199
surface structure3.32e-0799
endothelial tube6.83e-079
arterial system endothelium6.83e-079
endothelium of artery6.83e-079
tissue7.74e-07773
simple squamous epithelium8.39e-0722


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
FOS#235348.99795530889440.0001525147711168630.00195249940925154
FOXA1#3169411.08141974938556.62943068949433e-050.00107261210190565
JUN#3725412.51282919233634.07770316866756e-050.00074466032738673



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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