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Coexpression cluster:C3540

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Full id: C3540_skeletal_left_heart_Mesenchymal_diaphragm_Alveolar_tongue



Phase1 CAGE Peaks

  Short description
Hg19::chr16:2009500..2009584,+ p1@NDUFB10
Hg19::chr2:98262497..98262549,+ p1@COX5B
Hg19::chr3:48647059..48647102,- p1@UQCRC1


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


p.valueFDRnGenesnPathwayName
9.66492387457841e-081.52947420315203e-053132Oxidative phosphorylation (KEGG):00190
6.31961929821581e-050.0044447989064117931138Metabolic pathways (KEGG):01100
2.15074464693702e-050.00170177670188892277Cardiac muscle contraction (KEGG):04260
1.96661053766193e-072.48972894068001e-053167Alzheimer's disease (KEGG):05010
9.22896270049956e-081.52947420315203e-053130Parkinson's disease (KEGG):05012
2.59185625084851e-072.73440834464518e-053183Huntington's disease (KEGG):05016
5.41556645674944e-081.52947420315203e-053109Electron Transport Chain (Wikipathways):WP111
2.20095901611869e-081.39320705720313e-05381Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305
3.42164256458367e-060.000309414249054495231{CYCS,35} (Static Module):NA



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:0005743mitochondrial inner membrane3.94167936296023e-05
GO:0019866organelle inner membrane3.94167936296023e-05
GO:0031966mitochondrial membrane4.39079275427809e-05
GO:0005740mitochondrial envelope4.39079275427809e-05
GO:0044429mitochondrial part7.57771798962151e-05
GO:0031967organelle envelope7.57771798962151e-05
GO:0031975envelope7.57771798962151e-05
GO:0006118electron transport0.000104063478946275
GO:0005746mitochondrial respiratory chain0.000141381126508339
GO:0006091generation of precursor metabolites and energy0.000180464480492059
GO:0005739mitochondrion0.000198827660296956
GO:0044455mitochondrial membrane part0.000269873470898099
GO:0006119oxidative phosphorylation0.000430686169885607
GO:0031090organelle membrane0.00053948090000896
GO:0016491oxidoreductase activity0.000549886679035116
GO:0015078hydrogen ion transmembrane transporter activity0.000570691170457736
GO:0015077monovalent inorganic cation transmembrane transporter activity0.000619459136717262
GO:0022890inorganic cation transmembrane transporter activity0.000924073405410639
GO:0044446intracellular organelle part0.00772108058328133
GO:0044422organelle part0.00772108058328133
GO:0008324cation transmembrane transporter activity0.00792935597784679
GO:0016681oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor0.00822131044074366
GO:0008121ubiquinol-cytochrome-c reductase activity0.00822131044074366
GO:0016679oxidoreductase activity, acting on diphenols and related substances as donors0.00822131044074366
GO:0044444cytoplasmic part0.00846379679961598
GO:0007585respiratory gaseous exchange0.00846379679961598
GO:0045271respiratory chain complex I0.0103427143324249
GO:0030964NADH dehydrogenase complex (quinone)0.0103427143324249
GO:0005747mitochondrial respiratory chain complex I0.0103427143324249
GO:0004129cytochrome-c oxidase activity0.0103427143324249
GO:0016675oxidoreductase activity, acting on heme group of donors0.0103427143324249
GO:0016676oxidoreductase activity, acting on heme group of donors, oxygen as acceptor0.0103427143324249
GO:0015002heme-copper terminal oxidase activity0.0103427143324249
GO:0015075ion transmembrane transporter activity0.0110499762773029
GO:0009060aerobic respiration0.0110499762773029
GO:0006120mitochondrial electron transport, NADH to ubiquinone0.0113739705753752
GO:0016310phosphorylation0.0114123006757427
GO:0045333cellular respiration0.0115721504980818
GO:0022891substrate-specific transmembrane transporter activity0.0128118673586426
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0128118673586426
GO:0003954NADH dehydrogenase activity0.0128118673586426
GO:0050136NADH dehydrogenase (quinone) activity0.0128118673586426
GO:0042775organelle ATP synthesis coupled electron transport0.0128469912276672
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0128469912276672
GO:0022857transmembrane transporter activity0.0128469912276672
GO:0042773ATP synthesis coupled electron transport0.0128484456315034
GO:0006793phosphorus metabolic process0.0129587858695853
GO:0006796phosphate metabolic process0.0129587858695853
GO:0022892substrate-specific transporter activity0.013728668980004
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.016352482504285
GO:0015980energy derivation by oxidation of organic compounds0.017363226964559
GO:0005737cytoplasm0.0176623737467382
GO:0004222metalloendopeptidase activity0.0274222150223631
GO:0043231intracellular membrane-bound organelle0.0274222150223631
GO:0043227membrane-bound organelle0.0274222150223631
GO:0009055electron carrier activity0.0340569250592044
GO:0016020membrane0.0356268822602444
GO:0043229intracellular organelle0.0464093602139209
GO:0043226organelle0.0464093602139209
GO:0008237metallopeptidase activity0.0471924897371985



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
multi-tissue structure1.18e-18342
epithelial vesicle2.94e-1478
mesenchyme5.74e-14160
entire embryonic mesenchyme5.74e-14160
epithelium1.72e-12306
cell layer3.88e-12309
organism subdivision4.00e-12264
dense mesenchyme tissue7.55e-1273
paraxial mesoderm7.80e-1272
presumptive paraxial mesoderm7.80e-1272
trunk mesenchyme9.01e-12122
somite1.33e-1171
presomitic mesoderm1.33e-1171
presumptive segmental plate1.33e-1171
dermomyotome1.33e-1171
trunk paraxial mesoderm1.33e-1171
trunk1.64e-11199
anatomical cluster3.78e-11373
multilaminar epithelium1.77e-1083
muscle tissue1.19e-0964
musculature1.19e-0964
musculature of body1.19e-0964
skeletal muscle tissue1.21e-0962
striated muscle tissue1.21e-0962
myotome1.21e-0962
unilaminar epithelium1.62e-09148
organ part3.86e-09218
epithelial tube4.23e-09117
tube2.22e-08192
compound organ6.33e-0868
embryo1.24e-07592
anatomical conduit3.28e-07240


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
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
MA0073.10.0185922
MA0074.10.935474
MA0076.11.74184
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
MA0092.10.785956
MA0093.10.642957
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
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.11.37817
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CTCFL#140690213.16431623931620.007433367036996010.0306754156779211
E2F1#186934.907389214879320.008460985347239390.0324694781804275
E2F6#187635.017155731697390.00791769806886330.0321507180643085
EGR1#195834.988179094810140.008056488137383440.031998918599741
ELF1#199734.258097958807540.01295179875054610.0461316727954534
ETS1#211339.728760922202340.001085840092584840.00761152113762452
NFKB1#479035.488063424193840.006049381815655430.0269213988173359
NR3C1#290829.982015554115360.01278474365547170.0460343334816001
NRF1#4899312.21027944771090.0005492172401020010.00470547164388949
PAX5#507936.669565531177830.003370290999677260.0172679465127204
SIN3A#2594235.408884726815140.006318961977991520.0276116509777606
SMC3#9126210.02995522995520.0126656379767470.0457300202120404
STAT1#6772213.80439166479950.006770931708444080.0287494140219617
TAF7#6879311.43306940492390.0006690181981945830.0054185026445323
YY1#752834.911170749853860.008441455341808260.0328728570954589



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.