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Coexpression cluster:C534

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Full id: C534_Mesenchymal_Alveolar_Renal_Placental_Fibroblast_Smooth_Tracheal



Phase1 CAGE Peaks

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 cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>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 cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
embryonic cell2.84e-35248
animal cell1.57e-26679
eukaryotic cell1.57e-26679
epithelial cell1.98e-24254
mesodermal cell2.08e-24119
non-terminally differentiated cell2.92e-20180
contractile cell3.44e-1759
electrically responsive cell9.21e-1660
electrically active cell9.21e-1660
muscle cell1.36e-1454
somatic cell3.63e-14591
muscle precursor cell4.18e-1457
myoblast4.18e-1457
multi-potent skeletal muscle stem cell4.18e-1457
smooth muscle cell1.02e-1342
smooth muscle myoblast1.02e-1342
native cell1.34e-12722
vascular associated smooth muscle cell3.16e-1132
lining cell3.79e-1057
barrier cell3.79e-1057
meso-epithelial cell1.84e-0944
endothelial cell1.69e-0835
squamous epithelial cell2.63e-0862
ectodermal cell3.32e-0871
epithelial cell of nephron4.59e-0816
blood vessel endothelial cell7.87e-0818
embryonic blood vessel endothelial progenitor cell7.87e-0818
kidney cell1.05e-0718
kidney epithelial cell1.05e-0718
kidney cortical cell4.16e-0713
renal cortical epithelial cell4.16e-0713
endothelial cell of vascular tree7.82e-0724
Uber Anatomy
Ontology termp-valuen
trunk mesenchyme2.67e-18143
multilaminar epithelium1.05e-1782
somite6.76e-1783
paraxial mesoderm6.76e-1783
presomitic mesoderm6.76e-1783
presumptive segmental plate6.76e-1783
trunk paraxial mesoderm6.76e-1783
presumptive paraxial mesoderm6.76e-1783
trunk7.31e-17216
dermomyotome1.17e-1670
mesenchyme1.19e-16238
entire embryonic mesenchyme1.19e-16238
unilaminar epithelium4.36e-16138
epithelial tube9.78e-16118
vasculature1.01e-1479
vascular system1.01e-1479
skeletal muscle tissue1.67e-1361
striated muscle tissue1.67e-1361
myotome1.67e-1361
vessel3.95e-1369
blood vessel6.54e-1360
epithelial tube open at both ends6.54e-1360
blood vasculature6.54e-1360
vascular cord6.54e-1360
cell layer1.01e-12312
artery1.12e-1242
arterial blood vessel1.12e-1242
arterial system1.12e-1242
muscle tissue2.50e-1263
musculature2.50e-1263
musculature of body2.50e-1263
epithelium3.19e-12309
splanchnic layer of lateral plate mesoderm3.37e-1284
multi-tissue structure1.52e-10347
systemic artery1.41e-0833
systemic arterial system1.41e-0833
circulatory system2.55e-08113
nephron epithelium4.59e-0816
nephron4.59e-0816
uriniferous tubule4.59e-0816
metanephric mesenchyme4.59e-0816
nephrogenic mesenchyme4.59e-0816
cardiovascular system6.12e-08110
organism subdivision7.07e-08365
endothelium7.87e-0818
blood vessel endothelium7.87e-0818
cardiovascular system endothelium7.87e-0818
subdivision of trunk8.30e-08113
simple squamous epithelium1.08e-0722
squamous epithelium1.44e-0725
excretory tube3.20e-0717
mesonephric epithelium3.20e-0717
mesonephric tubule3.20e-0717
nephric duct3.20e-0717
kidney epithelium3.20e-0717
renal duct3.20e-0717
mesonephric duct3.20e-0717
pronephric duct3.20e-0717
parenchyma3.69e-0717
cortex of kidney4.16e-0713
renal parenchyma4.16e-0713
cortex7.48e-0716
urinary system structure8.11e-0744


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>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 cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C534&oldid=2131175"