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Coexpression cluster:C3123

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Full id: C3123_basal_Adipocyte_Preadipocyte_Olfactory_serous_mesenchymal_Smooth



Phase1 CAGE Peaks

  Short description
Hg19::chr11:18416103..18416118,+ p1@LDHA
Hg19::chr11:18416135..18416147,+ p2@LDHA
Hg19::chr9:14922428..14922432,- p1@LDHAP4


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:0004459L-lactate dehydrogenase activity0.00333608069390478
GO:0019642anaerobic glycolysis0.00333608069390478
GO:0004457lactate dehydrogenase activity0.00333608069390478
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.00800659366537148
GO:0006096glycolysis0.0137255891406368
GO:0006007glucose catabolic process0.0137255891406368
GO:0019320hexose catabolic process0.0137255891406368
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0137255891406368
GO:0046365monosaccharide catabolic process0.0137255891406368
GO:0046164alcohol catabolic process0.0137255891406368
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0137255891406368
GO:0044275cellular carbohydrate catabolic process0.0137255891406368
GO:0016052carbohydrate catabolic process0.0137255891406368
GO:0006006glucose metabolic process0.0137255891406368
GO:0019318hexose metabolic process0.0171391145649358
GO:0005996monosaccharide metabolic process0.0171391145649358
GO:0006066alcohol metabolic process0.0261980454491934
GO:0044262cellular carbohydrate metabolic process0.0275490032038769
GO:0044265cellular macromolecule catabolic process0.0275490032038769
GO:0005829cytosol0.0284234075120688
GO:0009057macromolecule catabolic process0.029786434767007
GO:0005975carbohydrate metabolic process0.03520290367003
GO:0044248cellular catabolic process0.03520290367003
GO:0009056catabolic process0.0405750814396169



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
disease_data


Cell Type
Ontology termp-valuen
animal cell2.14e-28679
eukaryotic cell2.14e-28679
somatic cell3.04e-19588
native cell2.57e-17722
fibroblast1.72e-1376
vascular associated smooth muscle cell1.31e-0932
stem cell5.90e-09441
somatic stem cell7.04e-09433
skin fibroblast7.79e-0923
multi fate stem cell1.05e-08427
non-terminally differentiated cell3.17e-08106
embryonic cell6.33e-08250
muscle precursor cell1.66e-0758
myoblast1.66e-0758
multi-potent skeletal muscle stem cell1.66e-0758
smooth muscle cell6.34e-0743
smooth muscle myoblast6.34e-0743
muscle cell8.89e-0755
Uber Anatomy
Ontology termp-valuen
artery5.30e-1142
arterial blood vessel5.30e-1142
arterial system5.30e-1142
integument1.23e-0946
integumental system1.23e-0946
multilaminar epithelium4.01e-0983
unilaminar epithelium4.98e-09148
somite1.08e-0871
presomitic mesoderm1.08e-0871
presumptive segmental plate1.08e-0871
dermomyotome1.08e-0871
trunk paraxial mesoderm1.08e-0871
systemic artery1.36e-0833
systemic arterial system1.36e-0833
skin of body1.96e-0841
surface structure2.06e-0899
dense mesenchyme tissue2.70e-0873
paraxial mesoderm3.65e-0872
presumptive paraxial mesoderm3.65e-0872
splanchnic layer of lateral plate mesoderm1.11e-0783
trunk1.15e-07199
epithelial tube open at both ends4.12e-0759
blood vessel4.12e-0759
blood vasculature4.12e-0759
vascular cord4.12e-0759
epithelial vesicle5.55e-0778
skeletal muscle tissue7.61e-0762
striated muscle tissue7.61e-0762
myotome7.61e-0762
Disease
Ontology termp-valuen
disease of cellular proliferation4.44e-07239
cancer7.08e-07235


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)
MA0003.10.178364
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.12.854
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.15.11284
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.13.02823
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.14.68342
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.24.26635
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.11.29138
MA0259.14.7418
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
BRCA1#672213.45615376214920.007119807716084560.0296107676831855
GTF2B#2959221.29588662288280.002878180589911410.0155740273887238
HNF4A#3172215.42152690863580.005444210486686610.0246686580337135
HNF4G#3174219.16894835096450.003543986611284220.0179666238384502
MAFF#23764237.54357099329680.0009344774015560320.00676762258796965
MAFK#7975218.06715542521990.003983674744936810.0191050652838525
MEF2A#4205212.4954872730960.008235029478029740.0324734092375287
NR3C1#290829.982015554115360.01278474365547170.0460105390294214
RDBP#79362102.4256026600170.0001264379392731220.00168260090975352
SMARCB1#6598212.16847718743830.008675002221921740.0329709435225185
STAT1#6772213.80439166479950.006770931708444080.0287435711201606
TAL1#6886219.91241111829350.003287176608740550.0170081465365496
ZEB1#6935211.25895467836260.01010222676646330.0377970359412001



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.