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Coexpression cluster:C3189

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Full id: C3189_Renal_Alveolar_Astrocyte_Hepatic_Smooth_Mesenchymal_Preadipocyte



Phase1 CAGE Peaks

  Short description
Hg19::chr11:65625678..65625687,- p2@CFL1
Hg19::chr5:176900590..176900601,- p2@DBN1
Hg19::chr5:176900610..176900662,- p1@DBN1


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:0030036actin cytoskeleton organization and biogenesis0.00172691235919777
GO:0030029actin filament-based process0.00172691235919777
GO:0042641actomyosin0.00172691235919777
GO:0003779actin binding0.00364878926538013
GO:0050773regulation of dendrite development0.00395429430057747
GO:0005522profilin binding0.00395429430057747
GO:0008092cytoskeletal protein binding0.00395429430057747
GO:0007010cytoskeleton organization and biogenesis0.00447896764911961
GO:0048168regulation of neuronal synaptic plasticity0.00518012705880347
GO:0016358dendrite development0.00621587796210872
GO:0048167regulation of synaptic plasticity0.00753395387979974
GO:0050803regulation of synapse structure and activity0.0077691611814973
GO:0048468cell development0.00904072481948437
GO:0005856cytoskeleton0.0109284430475919
GO:0006996organelle organization and biogenesis0.0115741645968369
GO:0050767regulation of neurogenesis0.0115741645968369
GO:0030425dendrite0.0115741645968369
GO:0007015actin filament organization0.0117936203516336
GO:0016363nuclear matrix0.0118891572824671
GO:0048869cellular developmental process0.0118891572824671
GO:0030154cell differentiation0.0118891572824671
GO:0043005neuron projection0.0190520721847851
GO:0043232intracellular non-membrane-bound organelle0.027080640390655
GO:0043228non-membrane-bound organelle0.027080640390655
GO:0031175neurite development0.0279208040194611
GO:0048666neuron development0.0302942956279923
GO:0016043cellular component organization and biogenesis0.0302942956279923
GO:0032502developmental process0.0302942956279923
GO:0006916anti-apoptosis0.0302942956279923
GO:0007266Rho protein signal transduction0.0319002373737859
GO:0032990cell part morphogenesis0.0319002373737859
GO:0030030cell projection organization and biogenesis0.0319002373737859
GO:0048858cell projection morphogenesis0.0319002373737859
GO:0030182neuron differentiation0.0319002373737859
GO:0043066negative regulation of apoptosis0.0325078441224394
GO:0043069negative regulation of programmed cell death0.0325078441224394
GO:0050793regulation of developmental process0.0325078441224394
GO:0048699generation of neurons0.0325078441224394
GO:0044446intracellular organelle part0.0325078441224394
GO:0044422organelle part0.0325078441224394
GO:0022008neurogenesis0.0329789957614248
GO:0007268synaptic transmission0.0355079027878207
GO:0015629actin cytoskeleton0.0355079027878207
GO:0042995cell projection0.0366846410436107
GO:0019226transmission of nerve impulse0.0378081004023087
GO:0007265Ras protein signal transduction0.0483452356566323



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
embryonic cell9.58e-35250
mesodermal cell6.54e-31121
non-terminally differentiated cell1.56e-20106
contractile cell5.61e-2059
electrically responsive cell5.93e-1961
electrically active cell5.93e-1961
muscle precursor cell2.41e-1858
myoblast2.41e-1858
multi-potent skeletal muscle stem cell2.41e-1858
muscle cell1.15e-1755
smooth muscle cell7.26e-1643
smooth muscle myoblast7.26e-1643
fibroblast8.31e-1676
animal cell3.25e-15679
eukaryotic cell3.25e-15679
somatic cell1.31e-13588
vascular associated smooth muscle cell1.34e-1332
meso-epithelial cell1.08e-1145
lining cell1.56e-1158
barrier cell1.56e-1158
endothelial cell8.82e-1136
ectodermal cell2.49e-0972
endothelial cell of vascular tree3.30e-0924
blood vessel endothelial cell6.29e-0918
embryonic blood vessel endothelial progenitor cell6.29e-0918
epithelial cell of nephron6.76e-0915
epithelial cell2.65e-08253
neurectodermal cell4.25e-0859
kidney cell2.03e-0717
kidney epithelial cell2.03e-0717
kidney cortical cell2.43e-0712
renal cortical epithelial cell2.43e-0712
Uber Anatomy
Ontology termp-valuen
vasculature4.15e-2578
vascular system4.15e-2578
cell layer1.34e-24309
epithelium2.51e-23306
epithelial vesicle2.03e-2278
vessel3.85e-2068
epithelial tube9.33e-20117
epithelial tube open at both ends1.44e-1959
blood vessel1.44e-1959
blood vasculature1.44e-1959
vascular cord1.44e-1959
multilaminar epithelium3.02e-1983
somite8.74e-1971
presomitic mesoderm8.74e-1971
presumptive segmental plate8.74e-1971
dermomyotome8.74e-1971
trunk paraxial mesoderm8.74e-1971
splanchnic layer of lateral plate mesoderm1.02e-1883
unilaminar epithelium1.15e-18148
dense mesenchyme tissue1.30e-1873
paraxial mesoderm1.63e-1872
presumptive paraxial mesoderm1.63e-1872
artery1.12e-1742
arterial blood vessel1.12e-1742
arterial system1.12e-1742
mesenchyme1.13e-17160
entire embryonic mesenchyme1.13e-17160
anatomical cluster4.69e-17373
skeletal muscle tissue1.35e-1662
striated muscle tissue1.35e-1662
myotome1.35e-1662
muscle tissue7.66e-1664
musculature7.66e-1664
musculature of body7.66e-1664
organism subdivision4.53e-15264
cardiovascular system8.85e-15109
trunk1.16e-14199
trunk mesenchyme1.39e-14122
systemic artery9.91e-1433
systemic arterial system9.91e-1433
circulatory system1.04e-13112
multi-cellular organism5.86e-13656
multi-tissue structure1.94e-12342
tube2.53e-11192
anatomical conduit6.12e-10240
anatomical system3.16e-09624
aorta4.99e-0921
aortic system4.99e-0921
anatomical group5.65e-09625
blood vessel endothelium6.29e-0918
endothelium6.29e-0918
cardiovascular system endothelium6.29e-0918
nephron epithelium6.76e-0915
renal tubule6.76e-0915
nephron tubule6.76e-0915
nephron6.76e-0915
uriniferous tubule6.76e-0915
nephrogenic mesenchyme6.76e-0915
parenchyma2.30e-0815
simple squamous epithelium2.40e-0822
excretory tube3.14e-0816
kidney epithelium3.14e-0816
squamous epithelium5.88e-0825
embryo1.27e-07592
integument2.32e-0746
integumental system2.32e-0746
cortex of kidney2.43e-0712
renal parenchyma2.43e-0712


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)
MA0003.14.57391
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.16.45108
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
MA0055.10.557638
MA0056.10
MA0057.10.886807
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
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0105.12.3269
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
MA0131.12.4174
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
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.12.04956
MA0062.21.141
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
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
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.17
MA0102.21.88331
MA0258.11.29138
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
E2F6#187635.017155731697390.00791769806886330.0320634536104697
FOSL1#8061226.47571981091530.001869833702590980.0110230053096014
TAF7#6879311.43306940492390.0006690181981945830.00540801792579288
ZNF143#7702313.50087655222790.0004062804962997170.00387856752770074



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.