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Coexpression cluster:C534

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Full id: C534_Mesenchymal_Alveolar_Renal_Placental_Fibroblast_Smooth_Tracheal



Phase1 CAGE Peaks

  Short description
Hg19::chr11:65655906..65655980,- p1@FIBP
Hg19::chr16:1823114..1823165,- p1@MRPS34
Hg19::chr16:1832923..1833008,+ p1@NUBP2
Hg19::chr16:2034183..2034223,+ p1@GFER
Hg19::chr16:30441293..30441370,- p1@DCTPP1
Hg19::chr16:420514..420555,- p1@MRPL28
Hg19::chr16:686295..686374,- p1@C16orf13
Hg19::chr16:838330..838397,- p1@RPUSD1
Hg19::chr19:1095330..1095381,- p1@POLR2E
Hg19::chr19:13068012..13068053,- p1@GADD45GIP1
Hg19::chr19:38865399..38865435,+ p1@PSMD8
Hg19::chr19:56186557..56186601,+ p1@EPN1
Hg19::chr1:1243966..1244033,+ p1@PUSL1
Hg19::chr1:1310530..1310603,- p1@AURKAIP1
Hg19::chr1:155179012..155179053,+ p1@MTX1
Hg19::chr1:2343951..2344018,- p1@PEX10
Hg19::chr22:37415776..37415843,+ p1@MPST


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:0001522pseudouridine synthesis0.00526578666000325
GO:0005739mitochondrion0.00526578666000325
GO:0009982pseudouridine synthase activity0.00608784549519806
GO:0043231intracellular membrane-bound organelle0.00608784549519806
GO:0043227membrane-bound organelle0.00608784549519806
GO:0009451RNA modification0.00608784549519806
GO:0016866intramolecular transferase activity0.0100573020919188
GO:0045839negative regulation of mitosis0.0100573020919188
GO:00167843-mercaptopyruvate sulfurtransferase activity0.0100573020919188
GO:0019754one-carbon compound catabolic process0.0139226257429952
GO:0016972thiol oxidase activity0.0139226257429952
GO:0009440cyanate catabolic process0.0139226257429952
GO:0009439cyanate metabolic process0.0139226257429952
GO:0043229intracellular organelle0.015407499101058
GO:0043226organelle0.015407499101058
GO:0016670oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor0.0212846537901441
GO:0004792thiosulfate sulfurtransferase activity0.0212846537901441
GO:0044444cytoplasmic part0.0215336050909609
GO:0044429mitochondrial part0.0215336050909609
GO:0044424intracellular part0.0215336050909609
GO:0045862positive regulation of proteolysis0.0215336050909609
GO:0017134fibroblast growth factor binding0.0235884805853947
GO:0016783sulfurtransferase activity0.0235884805853947
GO:0031980mitochondrial lumen0.0237277706888406
GO:0005759mitochondrial matrix0.0237277706888406
GO:0016558protein import into peroxisome matrix0.031280760004272
GO:0005838proteasome regulatory particle (sensu Eukaryota)0.040138139493848
GO:0005515protein binding0.045757987491814
GO:0006625protein targeting to peroxisome0.045757987491814
GO:0008543fibroblast growth factor receptor signaling pathway0.045757987491814
GO:0043574peroxisomal transport0.045757987491814
GO:0030162regulation of proteolysis0.045757987491814
GO:0005737cytoplasm0.045757987491814
GO:0031974membrane-enclosed lumen0.045757987491814
GO:0043233organelle lumen0.045757987491814
GO:0005743mitochondrial inner membrane0.045757987491814
GO:0016853isomerase activity0.045757987491814
GO:0019866organelle inner membrane0.0493032392319663



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 cell1.50e-34250
animal cell2.44e-26679
eukaryotic cell2.44e-26679
mesodermal cell5.71e-25121
epithelial cell4.01e-22253
non-terminally differentiated cell1.08e-17106
contractile cell7.19e-1759
electrically responsive cell1.28e-1561
electrically active cell1.28e-1561
muscle cell9.78e-1555
somatic cell1.31e-14588
muscle precursor cell2.78e-1458
myoblast2.78e-1458
multi-potent skeletal muscle stem cell2.78e-1458
smooth muscle cell2.02e-1343
smooth muscle myoblast2.02e-1343
native cell1.63e-12722
vascular associated smooth muscle cell2.09e-1132
lining cell2.59e-1058
barrier cell2.59e-1058
meso-epithelial cell1.03e-0945
endothelial cell8.84e-0936
epithelial cell of nephron1.40e-0815
kidney cell3.29e-0817
kidney epithelial cell3.29e-0817
squamous epithelial cell3.55e-0863
blood vessel endothelial cell8.87e-0818
embryonic blood vessel endothelial progenitor cell8.87e-0818
ectodermal cell1.13e-0772
kidney cortical cell1.42e-0712
renal cortical epithelial cell1.42e-0712
endothelial cell of vascular tree9.04e-0724
Uber Anatomy
Ontology termp-valuen
epithelial vesicle7.78e-2178
unilaminar epithelium5.67e-19148
multilaminar epithelium7.25e-1883
mesenchyme1.94e-17160
entire embryonic mesenchyme1.94e-17160
somite3.19e-1771
presomitic mesoderm3.19e-1771
presumptive segmental plate3.19e-1771
dermomyotome3.19e-1771
trunk paraxial mesoderm3.19e-1771
dense mesenchyme tissue6.26e-1773
paraxial mesoderm1.07e-1672
presumptive paraxial mesoderm1.07e-1672
trunk1.97e-16199
epithelial tube7.24e-16117
organism subdivision3.51e-15264
vasculature4.09e-1578
vascular system4.09e-1578
trunk mesenchyme8.43e-15122
skeletal muscle tissue3.78e-1462
striated muscle tissue3.78e-1462
myotome3.78e-1462
vessel9.06e-1468
epithelial tube open at both ends1.32e-1359
blood vessel1.32e-1359
blood vasculature1.32e-1359
vascular cord1.32e-1359
muscle tissue7.42e-1364
musculature7.42e-1364
musculature of body7.42e-1364
artery8.29e-1342
arterial blood vessel8.29e-1342
arterial system8.29e-1342
splanchnic layer of lateral plate mesoderm9.27e-1383
cell layer1.25e-12309
epithelium3.22e-12306
multi-tissue structure5.09e-09342
systemic artery1.00e-0833
systemic arterial system1.00e-0833
nephron epithelium1.40e-0815
renal tubule1.40e-0815
nephron tubule1.40e-0815
nephron1.40e-0815
uriniferous tubule1.40e-0815
nephrogenic mesenchyme1.40e-0815
circulatory system2.96e-08112
parenchyma3.14e-0815
cardiovascular system4.33e-08109
anatomical cluster5.29e-08373
blood vessel endothelium8.87e-0818
endothelium8.87e-0818
cardiovascular system endothelium8.87e-0818
simple squamous epithelium1.14e-0722
cortex of kidney1.42e-0712
renal parenchyma1.42e-0712
excretory tube1.49e-0716
kidney epithelium1.49e-0716
squamous epithelium1.90e-0725
urinary system structure2.88e-0747
subdivision of trunk3.09e-07112
cortex6.43e-0715
renal system8.43e-0748


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)
MA0003.19.44676
MA0004.10.221943
MA0006.11.20202
MA0007.10.208008
MA0009.10.621697
MA0014.19.1214
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.14.7783
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.345177
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.624776
MA0056.10
MA0057.11.16763
MA0058.10.153757
MA0059.11.45503
MA0060.12.1255
MA0061.10.356644
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.269471
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.16.02678
MA0074.10.298586
MA0076.16.39177
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.11.04103
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.195947
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.372085
MA0103.10.10701
MA0105.10.7537
MA0106.10.894258
MA0107.10.551112
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.25223
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.438293
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.11.81788
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.830767
MA0139.12.31631
MA0140.10.269307
MA0141.10.462123
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.11.49496
MA0146.14.02163
MA0147.11.4384
MA0148.10.240905
MA0149.10.261654
MA0062.29.7035
MA0035.20.268747
MA0039.24.85926
MA0138.20.38342
MA0002.20.0459391
MA0137.20.398112
MA0104.22.11927
MA0047.20.326636
MA0112.21.0853
MA0065.20.593175
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.137179
MA0155.11.7213
MA0156.11.30109
MA0157.10.421609
MA0158.10
MA0159.10.571105
MA0160.10.252705
MA0161.10
MA0162.15.86502
MA0163.14.06005
MA0164.10.361105
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.212.7069
MA0102.21.14323
MA0258.10.476351
MA0259.12.65713
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#46745.285452829649120.005857629621042940.0262943772024458
BCL3#60236.096547553600880.01216124763562880.0440948667482792
BCLAF1#977478.915796074756055.76542330868176e-060.000173176601937134
BRCA1#67255.936538424477580.001116803475174350.00766043860132232
CCNT2#905145.218048357498642.50272071132719e-092.11988360397648e-07
CHD2#110695.476247382767758.66603667249791e-060.000235083689360782
CTCF#1066482.522473587329420.007107635535135630.0296297588174682
CTCFL#14069066.969343891402720.0001282789271753550.00170536187312461
E2F1#1869113.175369491980749.04802704927931e-050.00132033938381959
E2F4#187496.706620166915291.60415012189843e-066.09442832233358e-05
E2F6#1876144.131775308456675.72092945550856e-083.57563226453536e-06
EGR1#1958144.1079121957266.17965026005095e-083.8234389425916e-06
ELF1#1997164.007621608289451.13144653180838e-091.04020373534802e-07
ELK4#200587.640320780455543.03218555346911e-060.000102651029827799
ETS1#2113137.439640705213552.27105563122036e-102.32992906747567e-08
GABPB1#2553135.404699404139311.23195590443172e-089.16411985063708e-07
HEY1#23462163.802457452334792.58316753849527e-092.17742885030595e-07
HMGN3#9324136.254183553150452.00190675212248e-091.72648339624211e-07
IRF1#3659146.289428973523211.99717530377116e-102.06517813416392e-08
IRF3#3661411.05457699093870.0003906279980140290.00382135607761214
JUND#372783.291606560880480.001260436186465030.00846442225297207
MAX#414983.0364967101210.002156018665435590.012444591212525
MXI1#460195.273773215225511.18160458251851e-050.00029916509331794
MYC#4609164.915088820338264.54175528985501e-115.1502321467662e-09
NFKB1#4790103.228272602466960.0002222895719987040.0024771340813031
NFYA#480055.419288441126620.001678186748202080.0104900733657815
NFYB#480154.929350956922490.002549594632595590.0141096393510837
NR2C2#7182611.51103914302627.66053794422864e-060.000218178053547122
PAX5#5079145.492583378617041.25245751600589e-091.14140846870977e-07
PBX3#509056.445444907865920.0007705128745074350.00604141096851967
POLR2A#5430172.147453176558072.27473247069268e-068.13041699201481e-05
POU2F2#545284.285234850702360.0002049413346799760.00243198137173526
RFX5#599353.543503184469150.01042396886042850.0386862188200241
RXRA#625644.723439326854890.008683952615939730.0330013582438006
SIN3A#25942165.090715037002482.6091191843489e-113.0755507730724e-09
SIX5#1479121111.05610993588522.44264174845305e-102.49615520123961e-08
SMC3#912676.194972347913526.13164858570721e-050.00100546906365627
SP1#6667124.022386855158282.1835477628908e-067.8420751309681e-05
SP2#666846.153771880904620.003405940261545220.0173586275119813
SRF#672275.681191049127920.0001063572568630990.00148163872876152
TAF1#6872173.343046285745291.22696034516851e-091.1191485719568e-07
TAF7#687985.380267955258314.02734747987804e-050.000738563904215948
TBP#6908143.052634683491143.08185039759894e-060.000103861043457514
THAP1#55145814.76195040134181.99399089791794e-081.42442144587997e-06
USF1#7391103.742058398357626.11289652105867e-050.00100286647779272
YY1#7528164.622278352803631.19680964744564e-101.28726676384733e-08
ZBTB33#1000947.450523536466150.001699918066298720.0106182860601778
ZBTB7A#51341135.622048294258047.55171478530207e-095.85084228829498e-07
ZEB1#693554.96718588751290.002465493332121750.0138526822742341
ZNF143#770297.147522880591249.38784177277639e-074.02321217442344e-05



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.