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Coexpression cluster:C3282: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!3.49e-31!79;UBERON:0007798!3.49e-31!79;UBERON:0004872!7.09e-29!84;UBERON:0000055!5.41e-28!69;UBERON:0004535!7.50e-26!110;UBERON:0001009!8.37e-26!113;UBERON:0001981!1.99e-24!60;UBERON:0007500!1.99e-24!60;UBERON:0004537!1.99e-24!60;UBERON:0006965!1.99e-24!60;UBERON:0003914!3.21e-24!118;UBERON:0000119!2.81e-20!312;UBERON:0000483!1.83e-19!309;UBERON:0000468!2.50e-19!659;UBERON:0005256!6.80e-19!143;UBERON:0000486!1.17e-18!82;UBERON:0000914!4.58e-18!83;UBERON:0002329!4.58e-18!83;UBERON:0003077!4.58e-18!83;UBERON:0003059!4.58e-18!83;UBERON:0007282!4.58e-18!83;UBERON:0009618!4.58e-18!83;UBERON:0007285!4.58e-18!83;UBERON:0000490!9.11e-18!138;UBERON:0001637!6.06e-17!42;UBERON:0003509!6.06e-17!42;UBERON:0004572!6.06e-17!42;UBERON:0004290!9.99e-17!70;UBERON:0002100!2.81e-16!216;UBERON:0000475!3.86e-16!365;UBERON:0000467!3.81e-15!625;UBERON:0000480!9.02e-15!626;UBERON:0002385!9.33e-15!63;UBERON:0001015!9.33e-15!63;UBERON:0000383!9.33e-15!63;UBERON:0000477!9.35e-15!286;UBERON:0001134!1.09e-14!61;UBERON:0002036!1.09e-14!61;UBERON:0003082!1.09e-14!61;UBERON:0004111!1.72e-14!241;UBERON:0004573!5.21e-14!33;UBERON:0004571!5.21e-14!33;UBERON:0000481!1.49e-13!347;UBERON:0001986!3.67e-12!18;UBERON:0004638!3.67e-12!18;UBERON:0004852!3.67e-12!18;UBERON:0003104!4.28e-12!238;UBERON:0009142!4.28e-12!238;UBERON:0006914!1.24e-11!25;UBERON:0000487!9.09e-11!22;UBERON:0000922!1.13e-10!612;UBERON:0003103!1.71e-10!69;UBERON:0000025!2.29e-10!194;UBERON:0002050!4.77e-10!605;UBERON:0005423!4.77e-10!605;UBERON:0003102!5.17e-10!95;UBERON:0000923!7.50e-10!604;UBERON:0005291!7.50e-10!604;UBERON:0006598!7.50e-10!604;UBERON:0002532!7.50e-10!604;UBERON:0000947!2.98e-09!21;UBERON:0010191!2.98e-09!21;UBERON:0000926!3.52e-08!448;UBERON:0004120!3.52e-08!448;UBERON:0006603!3.52e-08!448;UBERON:0000948!1.07e-07!24;UBERON:0005498!1.07e-07!24;UBERON:0004140!1.07e-07!24;UBERON:0009881!1.07e-07!24;UBERON:0004141!1.07e-07!24;UBERON:0003084!1.07e-07!24;UBERON:0007005!1.07e-07!24;UBERON:0004139!1.07e-07!24;UBERON:0004291!1.07e-07!24;UBERON:0007100!1.61e-07!27;UBERON:0003915!7.80e-07!9;UBERON:0004700!7.80e-07!9;UBERON:0001917!7.80e-07!9
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}}

Revision as of 19:02, 8 August 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
vasculature3.49e-3179
vascular system3.49e-3179
splanchnic layer of lateral plate mesoderm7.09e-2984
vessel5.41e-2869
cardiovascular system7.50e-26110
circulatory system8.37e-26113
blood vessel1.99e-2460
epithelial tube open at both ends1.99e-2460
blood vasculature1.99e-2460
vascular cord1.99e-2460
epithelial tube3.21e-24118
cell layer2.81e-20312
epithelium1.83e-19309
multi-cellular organism2.50e-19659
trunk mesenchyme6.80e-19143
multilaminar epithelium1.17e-1882
somite4.58e-1883
paraxial mesoderm4.58e-1883
presomitic mesoderm4.58e-1883
presumptive segmental plate4.58e-1883
trunk paraxial mesoderm4.58e-1883
presumptive paraxial mesoderm4.58e-1883
unilaminar epithelium9.11e-18138
artery6.06e-1742
arterial blood vessel6.06e-1742
arterial system6.06e-1742
dermomyotome9.99e-1770
trunk2.81e-16216
organism subdivision3.86e-16365
anatomical system3.81e-15625
anatomical group9.02e-15626
muscle tissue9.33e-1563
musculature9.33e-1563
musculature of body9.33e-1563
anatomical cluster9.35e-15286
skeletal muscle tissue1.09e-1461
striated muscle tissue1.09e-1461
myotome1.09e-1461
anatomical conduit1.72e-14241
systemic artery5.21e-1433
systemic arterial system5.21e-1433
multi-tissue structure1.49e-13347
endothelium3.67e-1218
blood vessel endothelium3.67e-1218
cardiovascular system endothelium3.67e-1218
mesenchyme4.28e-12238
entire embryonic mesenchyme4.28e-12238
squamous epithelium1.24e-1125
simple squamous epithelium9.09e-1122
embryo1.13e-10612
compound organ1.71e-1069
tube2.29e-10194
embryonic structure4.77e-10605
developing anatomical structure4.77e-10605
surface structure5.17e-1095
germ layer7.50e-10604
embryonic tissue7.50e-10604
presumptive structure7.50e-10604
epiblast (generic)7.50e-10604
aorta2.98e-0921
aortic system2.98e-0921
mesoderm3.52e-08448
mesoderm-derived structure3.52e-08448
presumptive mesoderm3.52e-08448
heart1.07e-0724
primitive heart tube1.07e-0724
primary heart field1.07e-0724
anterior lateral plate mesoderm1.07e-0724
heart tube1.07e-0724
heart primordium1.07e-0724
cardiac mesoderm1.07e-0724
cardiogenic plate1.07e-0724
heart rudiment1.07e-0724
primary circulatory organ1.61e-0727


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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