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Coexpression cluster:C4556

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Full id: C4556_Cardiac_heart_Adipocyte_Smooth_left_Fibroblast_skeletal



Phase1 CAGE Peaks

  Short description
Hg19::chr6:129204259..129204300,+ p1@LAMA2
Hg19::chr6:129204301..129204323,+ p2@LAMA2
Hg19::chr6:129204337..129204348,+ p5@LAMA2


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


No GOStat results

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


Cell Type
Ontology termp-valuen
fibroblast1.49e-1476
muscle precursor cell8.05e-1158
myoblast8.05e-1158
multi-potent skeletal muscle stem cell8.05e-1158
contractile cell7.09e-1059
muscle cell1.85e-0955
fat cell9.43e-0915
electrically responsive cell1.72e-0861
electrically active cell1.72e-0861
skin fibroblast2.68e-0723
Uber Anatomy
Ontology termp-valuen
adult organism1.16e-26114
structure with developmental contribution from neural crest3.48e-17132
multi-tissue structure3.69e-16342
multi-cellular organism4.08e-15656
dense mesenchyme tissue2.01e-1473
paraxial mesoderm3.91e-1472
presumptive paraxial mesoderm3.91e-1472
somite6.66e-1471
presomitic mesoderm6.66e-1471
presumptive segmental plate6.66e-1471
dermomyotome6.66e-1471
trunk paraxial mesoderm6.66e-1471
muscle tissue1.18e-1364
musculature1.18e-1364
musculature of body1.18e-1364
cell layer4.61e-13309
skeletal muscle tissue6.32e-1362
striated muscle tissue6.32e-1362
myotome6.32e-1362
primary circulatory organ9.95e-1327
epithelium2.65e-12306
epithelial vesicle7.88e-1278
anatomical cluster1.33e-11373
neural plate2.03e-1182
presumptive neural plate2.03e-1182
tissue2.77e-11773
anatomical system5.16e-11624
anatomical group7.92e-11625
neural tube9.53e-1156
neural rod9.53e-1156
future spinal cord9.53e-1156
neural keel9.53e-1156
heart1.20e-1024
primitive heart tube1.20e-1024
primary heart field1.20e-1024
anterior lateral plate mesoderm1.20e-1024
heart tube1.20e-1024
heart primordium1.20e-1024
cardiac mesoderm1.20e-1024
cardiogenic plate1.20e-1024
heart rudiment1.20e-1024
multilaminar epithelium1.52e-1083
anatomical conduit4.21e-10240
central nervous system6.12e-1081
neurectoderm8.65e-1086
regional part of nervous system1.26e-0953
regional part of brain1.26e-0953
brain1.56e-0968
future brain1.56e-0968
trunk mesenchyme2.73e-09122
nervous system1.53e-0889
mesenchyme1.59e-08160
entire embryonic mesenchyme1.59e-08160
tube3.55e-08192
ecto-epithelium4.99e-08104
germ layer8.93e-08560
germ layer / neural crest8.93e-08560
embryonic tissue8.93e-08560
presumptive structure8.93e-08560
germ layer / neural crest derived structure8.93e-08560
epiblast (generic)8.93e-08560
embryonic structure1.30e-07564
organism subdivision1.48e-07264
splanchnic layer of lateral plate mesoderm2.02e-0783
regional part of forebrain2.36e-0741
forebrain2.36e-0741
anterior neural tube2.36e-0741
future forebrain2.36e-0741
organ2.43e-07503
ectoderm-derived structure6.43e-07171
ectoderm6.43e-07171
presumptive ectoderm6.43e-07171


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
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.16.81928
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.12.0778
MA0072.11.29561
MA0073.10.0185922
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
MA0092.10.785956
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
MA0144.10.531867
MA0145.14.82347
MA0146.10.707589
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.22.13189
MA0047.20.973066
MA0112.21.34467
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
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
CTCF#1066435.360256373075030.0064925092527670.0281030824705626
NRF1#4899312.21027944771090.0005492172401020010.00473147730256644
RAD21#5885310.35503389545630.0009004912073565420.00667943190377201



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.