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Coexpression cluster:C447

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Full id: C447_Alveolar_Bronchial_Smooth_Renal_Tracheal_Keratocytes_Hepatic



Phase1 CAGE Peaks

  Short description
Hg19::chr11:62341318..62341402,- p1@EEF1G
Hg19::chr14:23299088..23299114,+ p1@MRPL52
Hg19::chr17:49230905..49231005,+ p1@NME1
p3@NME1-NME2
p3@NME2
Hg19::chr17:7210852..7210861,+ p5@EIF5A
Hg19::chr17:7210877..7210888,+ p4@EIF5A
Hg19::chr17:7210898..7210918,+ p2@EIF5A
Hg19::chr17:79670386..79670427,+ p2@MRPL12
p2@SLC25A10
Hg19::chr19:1438351..1438382,+ p2@RPS15
Hg19::chr19:1438383..1438409,+ p1@RPS15
Hg19::chr19:17970693..17970729,+ p1@RPL18A
Hg19::chr19:42364267..42364301,+ p2@RPS19
Hg19::chr19:5690266..5690296,+ p2@RPL36
Hg19::chr20:60962115..60962126,+ p2@RPS21
Hg19::chr22:24236562..24236621,+ p1@MIF
Hg19::chr22:30987849..30987904,- p1@PES1
Hg19::chr2:73461410..73461463,+ p1@CCT7
Hg19::chr3:23958612..23958630,+ p1@RPL15
Hg19::chr3:39448443..39448499,+ p@chr3:39448443..39448499
+
Hg19::chr3:52029945..52029956,- p3@RPL29
Hg19::chr3:52029958..52029974,- p2@RPL29
Hg19::chr5:177580855..177580927,- p1@NHP2
Hg19::chr9:132388423..132388477,+ p1@METTL11A


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
1.80279937805575e-143.08438677416343e-12792Ribosome (KEGG):03010
0.0004045066255997470.0284502993338489257Translation Factors (Wikipathways):WP107
1.94905957293108e-143.08438677416343e-12793Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
3.54069343756762e-172.24125894598031e-1410296Metabolism of proteins (Reactome):REACT_17015
8.42175523584154e-141.06619421285754e-117114Regulation of beta-cell development (Reactome):REACT_13698
1.23159185623497e-111.1137109214239e-098421Gene Expression (Reactome):REACT_71
1.0400835009089e-108.22966070094168e-097312Diabetes pathways (Reactome):REACT_15380
4.24738473644491e-134.48099089694938e-117143Influenza Infection (Reactome):REACT_6167
1.51898137154035e-154.80757604092522e-138138{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:0044249cellular biosynthetic process1.63536519439817e-12
GO:0033279ribosomal subunit2.59202003269642e-12
GO:0009058biosynthetic process8.6750274201438e-12
GO:0006412translation8.6750274201438e-12
GO:0005830cytosolic ribosome (sensu Eukaryota)2.4732840086186e-11
GO:0044445cytosolic part4.20728102009308e-11
GO:0009059macromolecule biosynthetic process8.32198503670861e-11
GO:0003735structural constituent of ribosome2.43550401320784e-10
GO:0005840ribosome4.71495388940078e-10
GO:0030529ribonucleoprotein complex5.71573379108332e-09
GO:0015934large ribosomal subunit1.81502338481676e-08
GO:0005829cytosol4.47144288756933e-08
GO:0032991macromolecular complex7.70890439572307e-07
GO:0043232intracellular non-membrane-bound organelle7.70890439572307e-07
GO:0043228non-membrane-bound organelle7.70890439572307e-07
GO:0044267cellular protein metabolic process1.78090254612308e-06
GO:0044260cellular macromolecule metabolic process1.94152835452668e-06
GO:0019538protein metabolic process2.6494594484899e-06
GO:0005737cytoplasm2.6494594484899e-06
GO:0044444cytoplasmic part2.91903608333342e-06
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)5.23508541645072e-06
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)7.62170201263084e-06
GO:0010467gene expression1.51581020644333e-05
GO:0003723RNA binding2.47431966682721e-05
GO:0044446intracellular organelle part0.000147606563219062
GO:0044422organelle part0.000147606563219062
GO:0005762mitochondrial large ribosomal subunit0.000178278722220159
GO:0000315organellar large ribosomal subunit0.000178278722220159
GO:0015935small ribosomal subunit0.000178278722220159
GO:0005515protein binding0.000207267769744039
GO:0044237cellular metabolic process0.000207267769744039
GO:0044238primary metabolic process0.000228281165093755
GO:0044424intracellular part0.000285289357924009
GO:0043233organelle lumen0.000339362993530787
GO:0031974membrane-enclosed lumen0.000339362993530787
GO:0005730nucleolus0.00036235080550322
GO:0043229intracellular organelle0.0011593666543526
GO:0043226organelle0.0011593666543526
GO:0000313organellar ribosome0.00152367751972329
GO:0005761mitochondrial ribosome0.00152367751972329
GO:0043170macromolecule metabolic process0.00155370022125681
GO:0005622intracellular0.00201124067833298
GO:0007000nucleolus organization and biogenesis0.0026693105552166
GO:0050178phenylpyruvate tautomerase activity0.0026693105552166
GO:0003676nucleic acid binding0.00282955004644999
GO:0051323metaphase0.0074936979378262
GO:0000089mitotic metaphase0.0074936979378262
GO:0005832chaperonin-containing T-complex0.00958180233340283
GO:0043030regulation of macrophage activation0.00958180233340283
GO:0032502developmental process0.0110492591165849
GO:0006390transcription from mitochondrial promoter0.0115051858477387
GO:0005759mitochondrial matrix0.0145227496622909
GO:0031980mitochondrial lumen0.0145227496622909
GO:0031981nuclear lumen0.0155820216738653
GO:0008135translation factor activity, nucleic acid binding0.0168141455663711
GO:0008283cell proliferation0.0185141408805772
GO:0042116macrophage activation0.0185141408805772
GO:0043022ribosome binding0.0192183727001798
GO:0001516prostaglandin biosynthetic process0.0192183727001798
GO:0046457prostanoid biosynthetic process0.0192183727001798
GO:0016862intramolecular oxidoreductase activity, interconverting keto- and enol-groups0.0192183727001798
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0221078039902013
GO:0006915apoptosis0.0243405685871074
GO:0012501programmed cell death0.0245085795362319
GO:0043234protein complex0.0261257076792559
GO:0016265death0.0263258028457658
GO:0008219cell death0.0263258028457658
GO:0048869cellular developmental process0.0263258028457658
GO:0030154cell differentiation0.0263258028457658
GO:0007566embryo implantation0.0272612887625557
GO:0043021ribonucleoprotein binding0.0272612887625557
GO:0006693prostaglandin metabolic process0.0272612887625557
GO:0006692prostanoid metabolic process0.0272612887625557
GO:0048522positive regulation of cellular process0.0276967443860152
GO:0022414reproductive process0.0276967443860152
GO:0050679positive regulation of epithelial cell proliferation0.0277197817017431
GO:0051272positive regulation of cell motility0.0314910633148022
GO:0040017positive regulation of locomotion0.0314910633148022
GO:0048518positive regulation of biological process0.0350683770571089
GO:0005853eukaryotic translation elongation factor 1 complex0.0350683770571089
GO:0044428nuclear part0.038465921753742
GO:0002274myeloid leukocyte activation0.038465921753742
GO:0019079viral genome replication0.0408006772958901
GO:0050678regulation of epithelial cell proliferation0.0416965439544594
GO:0015669gas transport0.0437543521028632
GO:0030218erythrocyte differentiation0.0437543521028632
GO:0046456icosanoid biosynthetic process0.0437543521028632
GO:0050673epithelial cell proliferation0.0437543521028632
GO:0046051UTP metabolic process0.0440157626532768
GO:0004550nucleoside diphosphate kinase activity0.0440157626532768
GO:0006228UTP biosynthetic process0.0440157626532768
GO:0009208pyrimidine ribonucleoside triphosphate metabolic process0.0440157626532768
GO:0046036CTP metabolic process0.0440157626532768
GO:0009209pyrimidine ribonucleoside triphosphate biosynthetic process0.0440157626532768
GO:0006241CTP biosynthetic process0.0440157626532768
GO:0048468cell development0.0440157626532768
GO:0046039GTP metabolic process0.0440157626532768
GO:0006183GTP biosynthetic process0.0440157626532768
GO:0006997nuclear organization and biogenesis0.0447395533592941
GO:0009220pyrimidine ribonucleotide biosynthetic process0.0466041472028266
GO:0009218pyrimidine ribonucleotide metabolic process0.047286560910938



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


Cell Type
Ontology termp-valuen
animal cell9.90e-37679
eukaryotic cell9.90e-37679
embryonic cell1.87e-33250
mesodermal cell9.89e-26121
epithelial cell7.18e-22253
native cell1.85e-20722
somatic cell1.65e-18588
contractile cell2.63e-1859
electrically responsive cell1.23e-1761
electrically active cell1.23e-1761
muscle precursor cell1.46e-1758
myoblast1.46e-1758
multi-potent skeletal muscle stem cell1.46e-1758
muscle cell5.17e-1755
non-terminally differentiated cell5.88e-17106
smooth muscle cell1.21e-1443
smooth muscle myoblast1.21e-1443
vascular associated smooth muscle cell4.76e-1232
squamous epithelial cell3.21e-0963
lining cell1.14e-0858
barrier cell1.14e-0858
epithelial cell of nephron1.43e-0715
meso-epithelial cell1.59e-0745
endothelial cell3.00e-0736
blood vessel endothelial cell6.57e-0718
embryonic blood vessel endothelial progenitor cell6.57e-0718
kidney cortical cell8.84e-0712
renal cortical epithelial cell8.84e-0712
Uber Anatomy
Ontology termp-valuen
epithelial vesicle3.56e-2278
unilaminar epithelium2.69e-19148
multilaminar epithelium5.40e-1983
somite1.18e-1871
presomitic mesoderm1.18e-1871
presumptive segmental plate1.18e-1871
dermomyotome1.18e-1871
trunk paraxial mesoderm1.18e-1871
paraxial mesoderm6.16e-1872
presumptive paraxial mesoderm6.16e-1872
dense mesenchyme tissue1.19e-1773
vasculature7.08e-1678
vascular system7.08e-1678
trunk7.27e-16199
epithelial tube1.23e-15117
skeletal muscle tissue3.48e-1562
striated muscle tissue3.48e-1562
myotome3.48e-1562
trunk mesenchyme8.07e-15122
organism subdivision8.95e-15264
epithelial tube open at both ends1.77e-1459
blood vessel1.77e-1459
blood vasculature1.77e-1459
vascular cord1.77e-1459
vessel1.93e-1468
mesenchyme3.01e-14160
entire embryonic mesenchyme3.01e-14160
artery6.73e-1442
arterial blood vessel6.73e-1442
arterial system6.73e-1442
muscle tissue1.20e-1364
musculature1.20e-1364
musculature of body1.20e-1364
splanchnic layer of lateral plate mesoderm4.28e-1383
cell layer1.89e-10309
epithelium7.28e-10306
systemic artery8.50e-1033
systemic arterial system8.50e-1033
cardiovascular system4.53e-09109
circulatory system2.90e-08112
nephron epithelium1.43e-0715
renal tubule1.43e-0715
nephron tubule1.43e-0715
nephron1.43e-0715
uriniferous tubule1.43e-0715
nephrogenic mesenchyme1.43e-0715
simple squamous epithelium1.99e-0722
parenchyma3.39e-0715
blood vessel endothelium6.57e-0718
endothelium6.57e-0718
cardiovascular system endothelium6.57e-0718
cortex of kidney8.84e-0712
renal parenchyma8.84e-0712
Disease
Ontology termp-valuen
disease of cellular proliferation7.71e-09239
cancer2.52e-08235


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)
MA0003.10.300123
MA0004.10.478761
MA0006.11.34653
MA0007.10.146569
MA0009.10.526253
MA0014.10.756514
MA0017.10.0884918
MA0019.10.262545
MA0024.11.94128
MA0025.10.647545
MA0027.12.09389
MA0028.15.46696
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.10.170492
MA0042.10.149889
MA0043.10.526535
MA0046.10.516541
MA0048.10.785687
MA0050.10.458935
MA0051.11.19882
MA0052.10.459414
MA0055.10.114719
MA0056.10
MA0057.10.1739
MA0058.10.682118
MA0059.10.678862
MA0060.10.795701
MA0061.10.214431
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.0112936
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.10.0207841
MA0074.10.639966
MA0076.14.57209
MA0077.10.49237
MA0078.10.30111
MA0081.11.12539
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.12.50869
MA0089.10
MA0090.10.118716
MA0091.10.160096
MA0092.11.35462
MA0093.10.530993
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.25283
MA0103.10.232452
MA0105.10.0646197
MA0106.10.719625
MA0107.10.369945
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.74833
MA0114.10.15638
MA0115.10.747865
MA0116.10.166035
MA0117.10.560027
MA0119.10.308642
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.660517
MA0139.13.18767
MA0140.11.72292
MA0141.10.100114
MA0142.10.359701
MA0143.10.272236
MA0144.10.0352516
MA0145.10.184458
MA0146.10.805278
MA0147.11.50005
MA0148.10.174705
MA0149.10.192747
MA0062.25.80326
MA0035.20.198962
MA0039.21.06886
MA0138.20.302079
MA0002.20.0227565
MA0137.20.0801516
MA0104.22.04086
MA0047.20.250458
MA0112.20.00940745
MA0065.20.192051
MA0150.10.369323
MA0151.10
MA0152.10.589582
MA0153.10.615584
MA0154.10.0194777
MA0155.10.00810476
MA0156.10.984489
MA0157.10.337287
MA0158.10
MA0159.10.170777
MA0160.10.18494
MA0161.10
MA0162.11.3611
MA0163.10.0106129
MA0164.10.28168
MA0080.20.9064
MA0018.20.260646
MA0099.20.204301
MA0079.20.334157
MA0102.21.03595
MA0258.10.032189
MA0259.12.06255
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
ATF3#46755.105266937729260.002433927964762810.0137070370834114
BCL3#60269.421937128292272.93418017155362e-050.000611662361151475
BCLAF1#97741312.7947463150721.44671795107775e-122.00124206745177e-10
BRCA1#6721110.09211532161191.85968539620785e-091.61047830094985e-07
CCNT2#905185.184164926605791.40740436129218e-111.72926945987052e-09
CEBPB#105182.898599136663570.003818968528619960.0188590124431671
CHD2#1106146.582559985347099.32019438683885e-108.6987648039952e-08
CTBP2#148838.55231822809020.004971522000771280.0232261590802304
CTCF#10664133.167424220453432.99857580791919e-050.000620626751492811
CTCFL#14069087.180536130536137.26091544726864e-060.000209134789960643
E2F1#1869132.899820899701427.94249971490149e-050.00121628552452287
E2F4#1874105.75820923422022.48863852364361e-068.77780880684953e-05
E2F6#1876132.964682932366646.23302721693576e-050.00102065087724922
EGR1#1958194.307972854608754.46740840578756e-115.07143115752225e-09
ELF1#1997193.677448237151967.99092056110953e-107.53896795376439e-08
ELK4#2005139.593811889094745.3476825898496e-115.99899701397747e-09
EP300#203382.463251536808440.01035214973756950.0384429016655532
ETS1#2113146.191029677765122.0922939384365e-091.79849454021703e-07
FOSL2#2355118.465100302280851.16412470769667e-088.71541364495575e-07
GABPB1#2553185.782650411421782.11525502887564e-122.87649895782218e-10
GATA1#2623127.396531714800248.245048586614e-096.35032912490692e-07
GTF2B#29591014.51992269742014.10690632324132e-104.03500648629351e-08
GTF2F1#2962158.686132415971122.62815715441991e-123.53714052900079e-10
HDAC2#3066116.707810118313131.27701774324178e-077.2999702291422e-06
HEY1#23462224.040111043105714.54670625232837e-147.40801020728428e-12
HMGN3#9324124.46102603091852.185436108535e-067.83807560917882e-05
HNF4A#317266.308806462623730.0002668060026345580.00285560074904187
HSF1#3297214.93551515151520.007887097992253930.0323802282799249
IRF1#3659206.942876139603553.85855617769904e-167.53240651668618e-14
JUNB#372645.565569574512930.00519357345170850.0240697411902811
JUND#3727134.133210511105611.44254818866034e-065.60902048680185e-05
KAT2A#2648256.00818181818180.0005936714178533510.00496894127337603
MAX#4149195.57266157596073.91874262967132e-135.76436002113018e-11
MEF2A#420575.96375528943220.000102708645113220.00143655928578808
MEF2C#420847.511155362295280.001769012733668810.0108710750745299
MXI1#4601177.697578076768551.6986893147028e-132.5899184428941e-11
MYC#4609225.22228187160941.60243654139612e-163.1999401519478e-14
NFKB1#4790215.238605995821395.36375379255986e-159.4307252919387e-13
NR2C2#718268.89489388324754.04724079652003e-050.000740781250521828
NRF1#4899147.770177830361491.0294984773122e-101.11419473027989e-08
PAX5#5079164.850593113583881.95025936842402e-091.68611869353341e-07
POLR2A#5430222.147453176558074.97800844931664e-083.19347803708956e-06
POU2F2#5452177.036550408255597.44477289518673e-131.06949743658928e-10
RAD21#588594.236150229959410.0001121264694098980.00154981158532297
RDBP#7936748.88494672409887.61769404990886e-118.37457209345717e-09
REST#5978156.579565033723651.41816839379657e-101.50673539043459e-08
RFX5#5993116.023955413597553.80510234599239e-071.8604919658853e-05
RXRA#625665.474895583399980.0005694627056446240.00485423730940408
SIN3A#25942184.425451140121482.15116950284204e-102.21564094385917e-08
SIX5#1479121612.42670207669759.9629857541958e-161.87481850303145e-13
SMC3#912696.154745254745265.65493765830361e-060.000170397009260119
SP1#6667205.180346707400821.22395104012673e-131.89937923744124e-11
SP2#666889.510374725034418.98564393383965e-073.86830860183957e-05
SPI1#6688124.475085550103312.11279115254993e-067.69647000980686e-05
SREBF1#672036.409888560066590.01095069375434060.0402902665049523
SRF#672295.644300198159561.14458402572262e-050.000291915045329535
STAT1#677276.588459658199745.47642093195201e-050.000927289114319287
STAT2#677338.899605161787370.004450921212738140.0210644263429925
TAF1#6872223.343046285745292.93491437348904e-123.90968778383701e-10
TAF7#6879199.874014486070659.23342203075802e-181.99654112519738e-15
TAL1#688645.43065757771640.005662389444849920.0255652036672437
TBP#6908223.706770687096393.02429873087763e-134.48657294253024e-11
TCF12#6938136.284001987655619.80686658086902e-097.43804893855758e-07
TCF7L2#6934104.895534801426071.07197462497178e-050.000278151448092988
THAP1#5514545.703480836882060.004763248668215220.0223863256079439
TRIM28#1015597.605214791243769.8309204284725e-074.1703147791602e-05
USF1#7391164.626544928878523.96319802964005e-093.2463720707261e-07
USF2#739284.724435412752580.0001467893777241970.00189523251577913
WRNIP1#56897314.97544968400580.001019755961599680.00723422720238477
YY1#7528184.018230613516791.12139614487522e-091.03187217598787e-07
ZBTB33#10009811.51444546544772.11708204037839e-071.12866733647309e-05
ZBTB7A#51341113.675954653937954.84020501263627e-050.000840549004514
ZEB1#693553.838280003987240.008194623156686470.0323531640215166
ZNF143#7702159.205143103791751.13490738382756e-121.58460684838992e-10
ZNF263#1012782.989760595276610.003140378022278250.0164879318454011
ZZZ3#26009554.41209373528033.11606059698663e-082.10367325590618e-06



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.