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Coexpression cluster:C3538

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Full id: C3538_iPS_Mallassezderived_Bronchial_HES3GFP_acute_chronic_hepatocellular



Phase1 CAGE Peaks

  Short description
Hg19::chr16:18801619..18801630,- p2@RPS15A
Hg19::chr2:55459808..55459860,+ p1@RPS27A
Hg19::chr3:197677089..197677100,+ p2@RPL35A


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
3.23952687815502e-081.05948726550059e-05392Ribosome (KEGG):03010
3.34751110742684e-081.05948726550059e-05393Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1037505066909e-060.000116445678455893296Metabolism of proteins (Reactome):REACT_17015
6.2031341872007e-081.30886131349935e-053114Regulation of beta-cell development (Reactome):REACT_13698
3.18533613032144e-060.0002520397213116843421Gene Expression (Reactome):REACT_71
1.29326205516739e-060.0001169478401315653312Diabetes pathways (Reactome):REACT_15380
1.23098667822397e-071.55842913463155e-053143Influenza Infection (Reactome):REACT_6167
1.10547371417187e-071.55842913463155e-053138{RPS27A,138} (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:0005830cytosolic ribosome (sensu Eukaryota)0.00204574031208939
GO:0044445cytosolic part0.00417978982585916
GO:0033279ribosomal subunit0.00417978982585916
GO:0008582regulation of synaptic growth at neuromuscular junction0.00417978982585916
GO:0051124synaptic growth at neuromuscular junction0.00417978982585916
GO:0042062long-term strengthening of neuromuscular junction0.00417978982585916
GO:0050806positive regulation of synaptic transmission0.0106074249154712
GO:0051971positive regulation of transmission of nerve impulse0.0106074249154712
GO:0031646positive regulation of neurological process0.0106074249154712
GO:0005829cytosol0.0106074249154712
GO:0007528neuromuscular junction development0.0106074249154712
GO:0030433ER-associated protein catabolic process0.0106074249154712
GO:0006515misfolded or incompletely synthesized protein catabolic process0.0106074249154712
GO:0048167regulation of synaptic plasticity0.0125334643717844
GO:0050804regulation of synaptic transmission0.0125334643717844
GO:0003735structural constituent of ribosome0.0125334643717844
GO:0051969regulation of transmission of nerve impulse0.0125334643717844
GO:0050803regulation of synapse structure and activity0.0125334643717844
GO:0005840ribosome0.0136205233382194
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0136205233382194
GO:0000049tRNA binding0.0136205233382194
GO:0031644regulation of neurological process0.0136205233382194
GO:0007416synaptogenesis0.0136205233382194
GO:0003723RNA binding0.014385426350698
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0164385508748134
GO:0048589developmental growth0.0164385508748134
GO:0030529ribonucleoprotein complex0.0164385508748134
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0164385508748134
GO:0050808synapse organization and biogenesis0.0164385508748134
GO:0006412translation0.0164385508748134
GO:0048741skeletal muscle fiber development0.0164385508748134
GO:0048747muscle fiber development0.0164385508748134
GO:0010467gene expression0.0177973724591936
GO:0044267cellular protein metabolic process0.0185390426406863
GO:0044260cellular macromolecule metabolic process0.0187151417405112
GO:0007411axon guidance0.0194746956104163
GO:0019538protein metabolic process0.019669226711609
GO:0007519skeletal muscle development0.0220666113673117
GO:0009059macromolecule biosynthetic process0.0224279650682972
GO:0016567protein ubiquitination0.022836552979904
GO:0032446protein modification by small protein conjugation0.0234975929219407
GO:0043062extracellular structure organization and biogenesis0.025018250826649
GO:0014706striated muscle development0.0255970539033313
GO:0015934large ribosomal subunit0.0296229750907722
GO:0044249cellular biosynthetic process0.0296229750907722
GO:0007409axonogenesis0.0303299924990499
GO:0048667neuron morphogenesis during differentiation0.0303299924990499
GO:0048812neurite morphogenesis0.0303299924990499
GO:0015935small ribosomal subunit0.0303299924990499
GO:0005737cytoplasm0.0303299924990499
GO:0000904cellular morphogenesis during differentiation0.03086667314336
GO:0031175neurite development0.0324268433209433
GO:0048666neuron development0.0362723634105823
GO:0009058biosynthetic process0.0390181141743141
GO:0007517muscle development0.0390181141743141
GO:0040008regulation of growth0.0430991616255652
GO:0032990cell part morphogenesis0.0430991616255652
GO:0048858cell projection morphogenesis0.0430991616255652
GO:0030030cell projection organization and biogenesis0.0430991616255652
GO:0030182neuron differentiation0.0433450960231335
GO:0005515protein binding0.0433450960231335
GO:0016477cell migration0.0463453531660582
GO:0043232intracellular non-membrane-bound organelle0.0463453531660582
GO:0043228non-membrane-bound organelle0.0463453531660582
GO:0048699generation of neurons0.046355984662957
GO:0022008neurogenesis0.0484043620897308
GO:0051239regulation of multicellular organismal process0.0484043620897308
GO:0045941positive regulation of transcription0.0484043620897308
GO:0006511ubiquitin-dependent protein catabolic process0.0484043620897308
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0484043620897308
GO:0019941modification-dependent protein catabolic process0.0484043620897308
GO:0043632modification-dependent macromolecule catabolic process0.0484043620897308
GO:0051603proteolysis involved in cellular protein catabolic process0.0484043620897308
GO:0007268synaptic transmission0.0484043620897308
GO:0044257cellular protein catabolic process0.0484043620897308



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


Uber Anatomy
Ontology termp-valuen
unilaminar epithelium3.76e-12148
epithelial vesicle1.14e-1078
trunk5.27e-10199
somite1.23e-0971
presomitic mesoderm1.23e-0971
presumptive segmental plate1.23e-0971
dermomyotome1.23e-0971
trunk paraxial mesoderm1.23e-0971
multilaminar epithelium1.25e-0983
paraxial mesoderm2.90e-0972
presumptive paraxial mesoderm2.90e-0972
dense mesenchyme tissue3.45e-0973
trunk mesenchyme7.05e-09122
organism subdivision1.93e-08264
mesenchyme3.94e-08160
entire embryonic mesenchyme3.94e-08160
skeletal muscle tissue4.48e-0862
striated muscle tissue4.48e-0862
myotome4.48e-0862
epithelial tube6.04e-08117
vasculature4.35e-0778
vascular system4.35e-0778
muscle tissue4.97e-0764
musculature4.97e-0764
musculature of body4.97e-0764
artery9.69e-0742
arterial blood vessel9.69e-0742
arterial system9.69e-0742
Disease
Ontology termp-valuen
cancer1.33e-23235
disease of cellular proliferation1.68e-23239
cell type cancer3.01e-12143
carcinoma1.17e-11106
organ system cancer3.08e-11137
hematologic cancer2.58e-0751
immune system cancer2.58e-0751


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)
MA0003.10.0471418
MA0004.10.826076
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
MA0055.10.190716
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
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.846801
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
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
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
E2F1#186934.907389214879320.008460985347239390.0324682851513938
ELF1#199734.258097958807540.01295179875054610.0461300995705857
GTF2B#2959331.94382993432423.06634405746243e-050.000627318133236668
GTF2F1#2962312.73966087675770.0004835525047438590.0043341692450175
KAT2A#26481205.3633333333330.004861545220737780.0227530773609067
MAX#414936.452555509007120.003721913834265510.0186263337455966
MYC#460935.22228187160940.007020843755740150.0293993785736637
NFKB1#479035.488063424193840.006049381815655430.026920251712695
POU2F2#545239.106124057742520.001324165192682130.00881081094282167
RFX5#5993312.04791082719510.0005717246050312580.00484033284896721
RXRA#6256213.38307809275550.007196434429465730.0298249371182131
SIN3A#2594235.408884726815140.006318961977991520.0276104957752262
SIX5#147912211.3911435703060.009873820081429030.0370672859627738
SP1#666735.69838137814090.005403962701712170.0246058534509359
STAT1#6772320.70658749719920.0001125992441046670.00154672529988785
TAF7#6879311.43306940492390.0006690181981945830.00541808247528257
YY1#752834.911170749853860.008441455341808260.0328716314110035
ZNF143#7702313.50087655222790.0004062804962997170.0038853153331239
ZZZ3#26009179.80440414507770.0124784379082580.0451587226411364



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.