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Coexpression cluster:C1780

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Full id: C1780_Mesenchymal_tenocyte_Osteoblast_Smooth_mature_Synoviocyte_Chondrocyte



Phase1 CAGE Peaks

  Short description
Hg19::chr17:40575190..40575206,- p4@PTRF
Hg19::chr17:40575209..40575222,- p2@PTRF
Hg19::chr17:40575228..40575241,- p3@PTRF
Hg19::chr17:46115174..46115183,- p2@COPZ2
Hg19::chr19:13106214..13106382,+ p1@NFIX


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:0042134rRNA primary transcript binding0.00629911987840746
GO:0003716RNA polymerase I transcription termination factor activity0.00629911987840746
GO:0006361transcription initiation from RNA polymerase I promoter0.00629911987840746
GO:0003715transcription termination factor activity0.00944812353844312
GO:0006353transcription termination0.0132262048248837
GO:0006360transcription from RNA polymerase I promoter0.0144102097285995
GO:0005801cis-Golgi network0.0144102097285995
GO:0030126COPI vesicle coat0.0144102097285995
GO:0030663COPI coated vesicle membrane0.0144102097285995
GO:0065003macromolecular complex assembly0.0144102097285995
GO:0030137COPI-coated vesicle0.0144102097285995
GO:0022607cellular component assembly0.0144102097285995
GO:0005783endoplasmic reticulum0.0144102097285995
GO:0016599caveolar membrane0.0144102097285995
GO:0043624cellular protein complex disassembly0.0144102097285995
GO:0043241protein complex disassembly0.0144102097285995
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0144102097285995
GO:0032984macromolecular complex disassembly0.0144102097285995
GO:0005901caveola0.0144102097285995
GO:0019843rRNA binding0.0169906068743104
GO:0022411cellular component disassembly0.0209212139325074
GO:0030120vesicle coat0.0209212139325074
GO:0030662coated vesicle membrane0.0209212139325074
GO:0005798Golgi-associated vesicle0.0271114120113892
GO:0006352transcription initiation0.0343031653617995
GO:0030659cytoplasmic vesicle membrane0.0364124261128975
GO:0044433cytoplasmic vesicle part0.0364124261128975
GO:0012506vesicle membrane0.0364124261128975
GO:0030117membrane coat0.0364124261128975
GO:0048475coated membrane0.0364124261128975
GO:0030135coated vesicle0.0446140550686479
GO:0005792microsome0.0476089978154376
GO:0042598vesicular fraction0.0481512019910992



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
dense mesenchyme tissue4.77e-2273
epithelial vesicle6.82e-2278
somite7.14e-2271
presomitic mesoderm7.14e-2271
presumptive segmental plate7.14e-2271
dermomyotome7.14e-2271
trunk paraxial mesoderm7.14e-2271
paraxial mesoderm1.50e-2172
presumptive paraxial mesoderm1.50e-2172
muscle tissue1.35e-2064
musculature1.35e-2064
musculature of body1.35e-2064
multilaminar epithelium2.99e-2083
skeletal muscle tissue2.99e-2062
striated muscle tissue2.99e-2062
myotome2.99e-2062
vasculature3.17e-2078
vascular system3.17e-2078
splanchnic layer of lateral plate mesoderm9.82e-2083
vessel2.18e-1868
epithelial tube open at both ends2.84e-1859
blood vessel2.84e-1859
blood vasculature2.84e-1859
vascular cord2.84e-1859
trunk mesenchyme6.79e-18122
mesenchyme9.81e-18160
entire embryonic mesenchyme9.81e-18160
organism subdivision5.33e-17264
artery9.89e-1742
arterial blood vessel9.89e-1742
arterial system9.89e-1742
unilaminar epithelium1.21e-16148
multi-tissue structure4.91e-15342
cell layer1.41e-14309
epithelium1.87e-14306
circulatory system2.45e-14112
multi-cellular organism2.78e-14656
epithelial tube3.87e-14117
cardiovascular system6.33e-14109
systemic artery1.16e-1333
systemic arterial system1.16e-1333
trunk1.19e-13199
anatomical cluster4.13e-13373
surface structure1.34e-1299
anatomical system1.69e-11624
anatomical group3.29e-11625
anatomical conduit4.08e-11240
integument9.15e-0946
integumental system9.15e-0946
aorta1.03e-0721
aortic system1.03e-0721
primary circulatory organ1.49e-0727
heart2.95e-0724
primitive heart tube2.95e-0724
primary heart field2.95e-0724
anterior lateral plate mesoderm2.95e-0724
heart tube2.95e-0724
heart primordium2.95e-0724
cardiac mesoderm2.95e-0724
cardiogenic plate2.95e-0724
heart rudiment2.95e-0724
tube3.95e-07192
mesoderm4.61e-07315
mesoderm-derived structure4.61e-07315
presumptive mesoderm4.61e-07315
skin of body4.92e-0741
adipose tissue6.39e-0714


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)
MA0003.11.40197
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.16.61106
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.12.23491
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.12.34702
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.11.25946
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.13.29691
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.868598
MA0146.10.6031
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.25.20522
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.425004
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.13.53221
MA0163.11.99104
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.28.2878
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
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
CCNT2#90545.068961261570110.002709998091280770.0148962889818564
CTBP2#1488337.63020020359693.95343056005017e-050.000737702937754297
E2F6#187644.013724585357910.006632118233933880.0282957553917162
ETS1#211335.83725655332140.009253279045631430.0349727937700105
FOS#235335.398773185336640.01153895317278740.0421900549787406
GTF2B#2959319.16629796059450.0002924229654472410.00310243418207481
NANOG#79923317.54686708860760.0003794200090681830.00376103325048139
NFYA#4800311.05534841989830.001470892907644430.0094117500540054
NFYB#4801310.05587595212190.001938165606725460.0113872681031053
REST#597835.790017229676810.009468788694433940.0356994629240095
SMC3#912639.02695970695970.002650964449467550.0146380499174126
TAF7#687936.859841642954350.005843286407019040.0262457848384079



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.