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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1237_Endothelial_Preadipocyte_Lymphatic_Renal_lung_heart_skin
|full_id=C1237_Endothelial_Preadipocyte_Lymphatic_Renal_lung_heart_skin
|gostat_on_coexpression_clusters=GO:0046982!protein heterodimerization activity!0.0432414929942305!6925$GO:0003714!transcription corepressor activity!0.0432414929942305!6925$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0432414929942305!6925$GO:0045892!negative regulation of transcription, DNA-dependent!0.0432414929942305!6925$GO:0005667!transcription factor complex!0.0432414929942305!6925$GO:0016564!transcription repressor activity!0.0432414929942305!6925$GO:0045893!positive regulation of transcription, DNA-dependent!0.0432414929942305!6925$GO:0045941!positive regulation of transcription!0.0432414929942305!6925$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0432414929942305!6925$GO:0016481!negative regulation of transcription!0.0432414929942305!6925$GO:0003712!transcription cofactor activity!0.0432414929942305!6925$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0432414929942305!6925$GO:0031325!positive regulation of cellular metabolic process!0.0432414929942305!6925$GO:0046983!protein dimerization activity!0.0432414929942305!6925$GO:0031324!negative regulation of cellular metabolic process!0.0432414929942305!6925$GO:0009893!positive regulation of metabolic process!0.0432414929942305!6925$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0432414929942305!6925$GO:0008134!transcription factor binding!0.0432414929942305!6925$GO:0009892!negative regulation of metabolic process!0.0432414929942305!6925$GO:0044451!nucleoplasm part!0.0432414929942305!6925$GO:0005654!nucleoplasm!0.0472868412642344!6925
|gostat_on_coexpression_clusters=GO:0046982!protein heterodimerization activity!0.0432414929942305!6925$GO:0003714!transcription corepressor activity!0.0432414929942305!6925$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0432414929942305!6925$GO:0045892!negative regulation of transcription, DNA-dependent!0.0432414929942305!6925$GO:0005667!transcription factor complex!0.0432414929942305!6925$GO:0016564!transcription repressor activity!0.0432414929942305!6925$GO:0045893!positive regulation of transcription, DNA-dependent!0.0432414929942305!6925$GO:0045941!positive regulation of transcription!0.0432414929942305!6925$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0432414929942305!6925$GO:0016481!negative regulation of transcription!0.0432414929942305!6925$GO:0003712!transcription cofactor activity!0.0432414929942305!6925$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0432414929942305!6925$GO:0031325!positive regulation of cellular metabolic process!0.0432414929942305!6925$GO:0046983!protein dimerization activity!0.0432414929942305!6925$GO:0031324!negative regulation of cellular metabolic process!0.0432414929942305!6925$GO:0009893!positive regulation of metabolic process!0.0432414929942305!6925$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0432414929942305!6925$GO:0008134!transcription factor binding!0.0432414929942305!6925$GO:0009892!negative regulation of metabolic process!0.0432414929942305!6925$GO:0044451!nucleoplasm part!0.0432414929942305!6925$GO:0005654!nucleoplasm!0.0472868412642344!6925

Revision as of 13:44, 12 September 2012


Full id: C1237_Endothelial_Preadipocyte_Lymphatic_Renal_lung_heart_skin



Phase1 CAGE Peaks

Hg19::chr18:53068893..53068902,-p28@TCF4
Hg19::chr18:53068911..53068935,-p4@TCF4
Hg19::chr18:53068940..53068951,-p21@TCF4
Hg19::chr18:53068982..53068993,-p20@TCF4
Hg19::chr2:225266779..225266786,-p4@FAM124B
Hg19::chr2:56412876..56412892,-p3@ENST00000432793
p3@uc010fca.1
Hg19::chr2:56412925..56412945,-p2@ENST00000432793
p2@uc010fca.1


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:0046982protein heterodimerization activity0.0432414929942305
GO:0003714transcription corepressor activity0.0432414929942305
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0432414929942305
GO:0045892negative regulation of transcription, DNA-dependent0.0432414929942305
GO:0005667transcription factor complex0.0432414929942305
GO:0016564transcription repressor activity0.0432414929942305
GO:0045893positive regulation of transcription, DNA-dependent0.0432414929942305
GO:0045941positive regulation of transcription0.0432414929942305
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0432414929942305
GO:0016481negative regulation of transcription0.0432414929942305
GO:0003712transcription cofactor activity0.0432414929942305
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0432414929942305
GO:0031325positive regulation of cellular metabolic process0.0432414929942305
GO:0046983protein dimerization activity0.0432414929942305
GO:0031324negative regulation of cellular metabolic process0.0432414929942305
GO:0009893positive regulation of metabolic process0.0432414929942305
GO:0006357regulation of transcription from RNA polymerase II promoter0.0432414929942305
GO:0008134transcription factor binding0.0432414929942305
GO:0009892negative regulation of metabolic process0.0432414929942305
GO:0044451nucleoplasm part0.0432414929942305
GO:0005654nucleoplasm0.0472868412642344



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
tube1.24e-30194
anatomical conduit2.29e-28241
splanchnic layer of lateral plate mesoderm1.88e-2684
anatomical cluster1.20e-25286
adult organism4.16e-25115
vessel4.48e-2569
vasculature2.37e-2479
vascular system2.37e-2479
blood vessel2.44e-2260
epithelial tube open at both ends2.44e-2260
blood vasculature2.44e-2260
vascular cord2.44e-2260
epithelium2.92e-22309
cell layer3.01e-22312
circulatory system2.65e-20113
regional part of nervous system2.47e-1994
nervous system2.47e-1994
cardiovascular system2.52e-19110
central nervous system5.10e-1982
neural tube1.92e-1857
neural rod1.92e-1857
future spinal cord1.92e-1857
neural keel1.92e-1857
regional part of brain4.67e-1759
brain5.51e-1769
future brain5.51e-1769
epithelial tube1.08e-16118
organism subdivision1.61e-16365
anterior neural tube7.03e-1642
multi-cellular organism1.99e-15659
regional part of forebrain2.62e-1541
forebrain2.62e-1541
future forebrain2.62e-1541
neural plate3.87e-1586
presumptive neural plate3.87e-1586
neurectoderm1.00e-1490
telencephalon3.23e-1434
endothelium5.30e-1418
blood vessel endothelium5.30e-1418
cardiovascular system endothelium5.30e-1418
gray matter8.65e-1434
brain grey matter8.65e-1434
regional part of telencephalon1.01e-1333
cerebral hemisphere1.25e-1332
artery1.38e-1342
arterial blood vessel1.38e-1342
arterial system1.38e-1342
anatomical system1.90e-12625
anatomical group3.14e-12626
simple squamous epithelium3.47e-1222
squamous epithelium4.06e-1225
unilaminar epithelium6.49e-12138
cerebral cortex1.05e-1125
pallium1.05e-1125
systemic artery2.90e-1133
systemic arterial system2.90e-1133
pre-chordal neural plate8.13e-1161
multi-tissue structure9.23e-11347
muscle tissue9.77e-1163
musculature9.77e-1163
musculature of body9.77e-1163
skeletal muscle tissue1.99e-1061
striated muscle tissue1.99e-1061
myotome1.99e-1061
regional part of cerebral cortex2.18e-1022
dermomyotome1.05e-0970
aorta1.44e-0921
aortic system1.44e-0921
neocortex1.63e-0920
primary circulatory organ3.10e-0827
endothelial tube8.13e-089
arterial system endothelium8.13e-089
endothelium of artery8.13e-089
heart2.66e-0724
primitive heart tube2.66e-0724
primary heart field2.66e-0724
anterior lateral plate mesoderm2.66e-0724
heart tube2.66e-0724
heart primordium2.66e-0724
cardiac mesoderm2.66e-0724


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
EP300#203343.870823843556110.01142567586684480.0418623456185722
FOS#235356.427110934924580.0002931195965424140.00310824627305241
GATA2#262459.103522666824285.45256227113712e-050.00092384839557964
GATA3#2625415.56372363268915.8119493323542e-050.000966859153108856
JUN#372558.93773513738315.96198127192225e-050.000984603671818925
POLR2A#543072.147453176558070.004747636447610280.0223471427326469
SUZ12#23512214.3187945460180.007819681923614860.03211986786834



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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