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Coexpression cluster:C3282: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0031269!pseudopodium formation!0.00423847294024064!148170$GO:0031268!pseudopodium organization and biogenesis!0.00423847294024064!148170$GO:0031274!positive regulation of pseudopodium formation!0.00423847294024064!148170$GO:0031272!regulation of pseudopodium formation!0.00423847294024064!148170$GO:0017049!GTP-Rho binding!0.00423847294024064!148170$GO:0030838!positive regulation of actin filament polymerization!0.00423847294024064!148170$GO:0031344!regulation of cell projection organization and biogenesis!0.00423847294024064!148170$GO:0031346!positive regulation of cell projection organization and biogenesis!0.00423847294024064!148170$GO:0030833!regulation of actin filament polymerization!0.0119282334752735!148170$GO:0030041!actin filament polymerization!0.0141190928522875!148170$GO:0017048!Rho GTPase binding!0.0141190928522875!148170$GO:0022603!regulation of anatomical structure morphogenesis!0.0141190928522875!148170$GO:0008360!regulation of cell shape!0.0141190928522875!148170$GO:0022604!regulation of cell morphogenesis!0.0141190928522875!148170$GO:0008064!regulation of actin polymerization and/or depolymerization!0.0141190928522875!148170$GO:0030832!regulation of actin filament length!0.0141190928522875!148170$GO:0032535!regulation of cellular component size!0.0141190928522875!148170$GO:0032956!regulation of actin cytoskeleton organization and biogenesis!0.0141190928522875!148170$GO:0030031!cell projection biogenesis!0.0141190928522875!148170$GO:0008430!selenium binding!0.0141190928522875!57190$GO:0051493!regulation of cytoskeleton organization and biogenesis!0.0143745331790643!148170$GO:0033043!regulation of organelle organization and biogenesis!0.0143745331790643!148170$GO:0008154!actin polymerization and/or depolymerization!0.0149760890815889!148170$GO:0007254!JNK cascade!0.0152923045578563!148170$GO:0031098!stress-activated protein kinase signaling pathway!0.0153575003160227!148170$GO:0017016!Ras GTPase binding!0.0167190430585973!148170$GO:0031267!small GTPase binding!0.017135774408785!148170$GO:0051247!positive regulation of protein metabolic process!0.017135774408785!148170$GO:0051020!GTPase binding!0.0182047674899782!148170$GO:0051258!protein polymerization!0.0182047674899782!148170$GO:0051128!regulation of cellular component organization and biogenesis!0.0182047674899782!148170$GO:0000165!MAPKKK cascade!0.0264343064197099!148170$GO:0007266!Rho protein signal transduction!0.0319306848958582!148170$GO:0032990!cell part morphogenesis!0.0319306848958582!148170$GO:0030030!cell projection organization and biogenesis!0.0319306848958582!148170$GO:0048858!cell projection morphogenesis!0.0319306848958582!148170$GO:0050793!regulation of developmental process!0.0359240784781714!148170$GO:0030036!actin cytoskeleton organization and biogenesis!0.0366031238167997!148170$GO:0030029!actin filament-based process!0.0375344561401569!148170$GO:0019899!enzyme binding!0.0429014915697675!148170
|gostat_on_coexpression_clusters=GO:0031269!pseudopodium formation!0.00423847294024064!148170$GO:0031268!pseudopodium organization and biogenesis!0.00423847294024064!148170$GO:0031274!positive regulation of pseudopodium formation!0.00423847294024064!148170$GO:0031272!regulation of pseudopodium formation!0.00423847294024064!148170$GO:0017049!GTP-Rho binding!0.00423847294024064!148170$GO:0030838!positive regulation of actin filament polymerization!0.00423847294024064!148170$GO:0031344!regulation of cell projection organization and biogenesis!0.00423847294024064!148170$GO:0031346!positive regulation of cell projection organization and biogenesis!0.00423847294024064!148170$GO:0030833!regulation of actin filament polymerization!0.0119282334752735!148170$GO:0030041!actin filament polymerization!0.0141190928522875!148170$GO:0017048!Rho GTPase binding!0.0141190928522875!148170$GO:0022603!regulation of anatomical structure morphogenesis!0.0141190928522875!148170$GO:0008360!regulation of cell shape!0.0141190928522875!148170$GO:0022604!regulation of cell morphogenesis!0.0141190928522875!148170$GO:0008064!regulation of actin polymerization and/or depolymerization!0.0141190928522875!148170$GO:0030832!regulation of actin filament length!0.0141190928522875!148170$GO:0032535!regulation of cellular component size!0.0141190928522875!148170$GO:0032956!regulation of actin cytoskeleton organization and biogenesis!0.0141190928522875!148170$GO:0030031!cell projection biogenesis!0.0141190928522875!148170$GO:0008430!selenium binding!0.0141190928522875!57190$GO:0051493!regulation of cytoskeleton organization and biogenesis!0.0143745331790643!148170$GO:0033043!regulation of organelle organization and biogenesis!0.0143745331790643!148170$GO:0008154!actin polymerization and/or depolymerization!0.0149760890815889!148170$GO:0007254!JNK cascade!0.0152923045578563!148170$GO:0031098!stress-activated protein kinase signaling pathway!0.0153575003160227!148170$GO:0017016!Ras GTPase binding!0.0167190430585973!148170$GO:0031267!small GTPase binding!0.017135774408785!148170$GO:0051247!positive regulation of protein metabolic process!0.017135774408785!148170$GO:0051020!GTPase binding!0.0182047674899782!148170$GO:0051258!protein polymerization!0.0182047674899782!148170$GO:0051128!regulation of cellular component organization and biogenesis!0.0182047674899782!148170$GO:0000165!MAPKKK cascade!0.0264343064197099!148170$GO:0007266!Rho protein signal transduction!0.0319306848958582!148170$GO:0032990!cell part morphogenesis!0.0319306848958582!148170$GO:0030030!cell projection organization and biogenesis!0.0319306848958582!148170$GO:0048858!cell projection morphogenesis!0.0319306848958582!148170$GO:0050793!regulation of developmental process!0.0359240784781714!148170$GO:0030036!actin cytoskeleton organization and biogenesis!0.0366031238167997!148170$GO:0030029!actin filament-based process!0.0375344561401569!148170$GO:0019899!enzyme binding!0.0429014915697675!148170
|id=C3282
|id=C3282
|ontology_enrichment_celltype=CL:0000055!3.07e-29!180;CL:0000222!2.00e-27!119;CL:0000220!3.39e-21!246;CL:0002321!3.55e-21!248;CL:0000115!5.40e-17!35;CL:0000183!7.04e-17!59;CL:0002078!2.89e-16!44;CL:0000057!1.11e-15!75;CL:0002139!1.14e-15!24;CL:0000187!9.80e-15!54;CL:0000680!1.17e-14!57;CL:0000056!1.17e-14!57;CL:0000355!1.17e-14!57;CL:0000213!2.66e-13!57;CL:0000215!2.66e-13!57;CL:0000192!1.20e-12!42;CL:0000514!1.20e-12!42;CL:0000393!1.75e-12!60;CL:0000211!1.75e-12!60;CL:0000071!3.67e-12!18;CL:0002546!3.67e-12!18;CL:0000359!1.14e-10!32;CL:0002371!6.28e-08!591;CL:0000144!6.16e-07!625;CL:1000413!7.80e-07!9
|ontology_enrichment_celltype=CL:0000222!3.69e-30!121;CL:0002321!4.75e-22!250;CL:0000183!6.92e-18!59;CL:0000115!4.62e-17!36;CL:0002078!5.13e-17!45;CL:0000057!5.25e-16!76;CL:0000187!6.54e-16!55;CL:0000680!1.03e-15!58;CL:0000056!1.03e-15!58;CL:0000355!1.03e-15!58;CL:0002139!7.79e-15!24;CL:0000055!3.67e-14!106;CL:0000213!5.87e-14!58;CL:0000215!5.87e-14!58;CL:0000192!9.42e-14!43;CL:0000514!9.42e-14!43;CL:0000393!2.74e-13!61;CL:0000211!2.74e-13!61;CL:0000071!4.28e-12!18;CL:0002546!4.28e-12!18;CL:0000359!1.40e-11!32;CL:0002371!1.47e-07!588;CL:1000413!6.48e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 14:57, 19 October 2012


Full id: C3282_Mesenchymal_Renal_Endothelial_Hepatic_Fibroblast_Pericytes_Trabecular



Phase1 CAGE Peaks

Hg19::chr12:48213650..48213695,-p1@HDAC7
Hg19::chr19:54984354..54984463,-p1@CDC42EP5
Hg19::chr1:26126670..26126721,+p1@SEPN1


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:0031269pseudopodium formation0.00423847294024064
GO:0031268pseudopodium organization and biogenesis0.00423847294024064
GO:0031274positive regulation of pseudopodium formation0.00423847294024064
GO:0031272regulation of pseudopodium formation0.00423847294024064
GO:0017049GTP-Rho binding0.00423847294024064
GO:0030838positive regulation of actin filament polymerization0.00423847294024064
GO:0031344regulation of cell projection organization and biogenesis0.00423847294024064
GO:0031346positive regulation of cell projection organization and biogenesis0.00423847294024064
GO:0030833regulation of actin filament polymerization0.0119282334752735
GO:0030041actin filament polymerization0.0141190928522875
GO:0017048Rho GTPase binding0.0141190928522875
GO:0022603regulation of anatomical structure morphogenesis0.0141190928522875
GO:0008360regulation of cell shape0.0141190928522875
GO:0022604regulation of cell morphogenesis0.0141190928522875
GO:0008064regulation of actin polymerization and/or depolymerization0.0141190928522875
GO:0030832regulation of actin filament length0.0141190928522875
GO:0032535regulation of cellular component size0.0141190928522875
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0141190928522875
GO:0030031cell projection biogenesis0.0141190928522875
GO:0008430selenium binding0.0141190928522875
GO:0051493regulation of cytoskeleton organization and biogenesis0.0143745331790643
GO:0033043regulation of organelle organization and biogenesis0.0143745331790643
GO:0008154actin polymerization and/or depolymerization0.0149760890815889
GO:0007254JNK cascade0.0152923045578563
GO:0031098stress-activated protein kinase signaling pathway0.0153575003160227
GO:0017016Ras GTPase binding0.0167190430585973
GO:0031267small GTPase binding0.017135774408785
GO:0051247positive regulation of protein metabolic process0.017135774408785
GO:0051020GTPase binding0.0182047674899782
GO:0051258protein polymerization0.0182047674899782
GO:0051128regulation of cellular component organization and biogenesis0.0182047674899782
GO:0000165MAPKKK cascade0.0264343064197099
GO:0007266Rho protein signal transduction0.0319306848958582
GO:0032990cell part morphogenesis0.0319306848958582
GO:0030030cell projection organization and biogenesis0.0319306848958582
GO:0048858cell projection morphogenesis0.0319306848958582
GO:0050793regulation of developmental process0.0359240784781714
GO:0030036actin cytoskeleton organization and biogenesis0.0366031238167997
GO:0030029actin filament-based process0.0375344561401569
GO:0019899enzyme binding0.0429014915697675



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
vasculature3.43e-3378
vascular system3.43e-3378
splanchnic layer of lateral plate mesoderm4.51e-3183
vessel1.36e-2968
epithelial tube1.31e-28117
epithelial tube open at both ends1.21e-2659
blood vessel1.21e-2659
blood vasculature1.21e-2659
vascular cord1.21e-2659
circulatory system3.40e-26112
cardiovascular system5.67e-26109
cell layer1.38e-22309
multi-cellular organism1.01e-21656
epithelium1.37e-21306
mesenchyme2.91e-21160
entire embryonic mesenchyme2.91e-21160
unilaminar epithelium3.47e-21148
epithelial vesicle9.91e-2178
organism subdivision4.92e-19264
artery1.54e-1842
arterial blood vessel1.54e-1842
arterial system1.54e-1842
anatomical cluster3.83e-18373
multilaminar epithelium5.75e-1883
anatomical system1.03e-17624
anatomical group2.65e-17625
somite3.61e-1771
presomitic mesoderm3.61e-1771
presumptive segmental plate3.61e-1771
dermomyotome3.61e-1771
trunk paraxial mesoderm3.61e-1771
trunk mesenchyme4.15e-17122
dense mesenchyme tissue8.09e-1773
paraxial mesoderm8.84e-1772
presumptive paraxial mesoderm8.84e-1772
trunk1.54e-16199
skeletal muscle tissue8.65e-1662
striated muscle tissue8.65e-1662
myotome8.65e-1662
anatomical conduit1.04e-15240
muscle tissue1.26e-1564
musculature1.26e-1564
musculature of body1.26e-1564
systemic artery5.88e-1533
systemic arterial system5.88e-1533
multi-tissue structure2.11e-13342
tube2.12e-12192
blood vessel endothelium4.28e-1218
endothelium4.28e-1218
cardiovascular system endothelium4.28e-1218
squamous epithelium5.37e-1225
compound organ7.96e-1268
simple squamous epithelium2.48e-1122
mesoderm6.10e-11315
mesoderm-derived structure6.10e-11315
presumptive mesoderm6.10e-11315
embryo8.50e-11592
aorta1.01e-1021
aortic system1.01e-1021
developing anatomical structure3.07e-10581
germ layer4.25e-09560
germ layer / neural crest4.25e-09560
embryonic tissue4.25e-09560
presumptive structure4.25e-09560
germ layer / neural crest derived structure4.25e-09560
epiblast (generic)4.25e-09560
embryonic structure6.97e-09564
primary circulatory organ3.73e-0827
heart4.43e-0824
primitive heart tube4.43e-0824
primary heart field4.43e-0824
anterior lateral plate mesoderm4.43e-0824
heart tube4.43e-0824
heart primordium4.43e-0824
cardiac mesoderm4.43e-0824
cardiogenic plate4.43e-0824
heart rudiment4.43e-0824


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.

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