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{{Coexpression_clusters
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Latest revision as of 02:40, 17 September 2013


Full id: C1237_Endothelial_Preadipocyte_Lymphatic_Renal_lung_heart_skin



Phase1 CAGE Peaks

  Short description
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 clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
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 clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
tube1.21e-27192
adult organism6.29e-26114
anatomical conduit5.62e-25240
anatomical cluster1.27e-23373
vessel3.14e-2368
splanchnic layer of lateral plate mesoderm4.82e-2183
epithelial tube open at both ends1.86e-2059
blood vessel1.86e-2059
blood vasculature1.86e-2059
vascular cord1.86e-2059
vasculature2.97e-2078
vascular system2.97e-2078
blood vessel endothelium5.93e-1918
endothelium5.93e-1918
cardiovascular system endothelium5.93e-1918
circulatory system5.53e-17112
epithelium1.44e-16306
cell layer5.10e-16309
neural tube6.66e-1656
neural rod6.66e-1656
future spinal cord6.66e-1656
neural keel6.66e-1656
cardiovascular system6.98e-16109
central nervous system8.32e-1681
epithelial tube6.56e-15117
multi-cellular organism7.08e-15656
nervous system7.82e-1589
telencephalon1.02e-1434
brain1.04e-1468
future brain1.04e-1468
brain grey matter1.56e-1434
gray matter1.56e-1434
regional part of forebrain2.33e-1441
forebrain2.33e-1441
anterior neural tube2.33e-1441
future forebrain2.33e-1441
regional part of nervous system2.42e-1453
regional part of brain2.42e-1453
simple squamous epithelium5.07e-1422
cerebral hemisphere5.27e-1432
regional part of telencephalon1.56e-1332
squamous epithelium5.62e-1325
neurectoderm3.57e-1286
neural plate9.65e-1282
presumptive neural plate9.65e-1282
artery3.86e-1142
arterial blood vessel3.86e-1142
arterial system3.86e-1142
anatomical system1.35e-10624
cerebral cortex1.36e-1025
pallium1.36e-1025
anatomical group1.75e-10625
structure with developmental contribution from neural crest2.53e-10132
endothelial tube2.54e-109
arterial system endothelium2.54e-109
endothelium of artery2.54e-109
aorta3.41e-1021
aortic system3.41e-1021
systemic artery1.67e-0933
systemic arterial system1.67e-0933
pre-chordal neural plate6.08e-0961
neocortex6.51e-0920
regional part of cerebral cortex1.07e-0822
multi-tissue structure4.62e-08342
germ layer6.51e-08560
germ layer / neural crest6.51e-08560
embryonic tissue6.51e-08560
presumptive structure6.51e-08560
germ layer / neural crest derived structure6.51e-08560
epiblast (generic)6.51e-08560
embryonic structure7.37e-08564
vein1.43e-079
venous blood vessel1.43e-079
venous system1.43e-079
unilaminar epithelium2.39e-07148
developing anatomical structure3.43e-07581
organ system subdivision6.60e-07223
ecto-epithelium7.70e-07104
embryo7.78e-07592


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.13.11883
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.11.47594
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.12.75658
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.11.11391
MA0091.11.26109
MA0092.14.12807
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.11.59862
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.11.83545
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.591589
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.071478
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.382702
MA0164.10.678332
MA0080.21.63199
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

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 clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.