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Coexpression cluster:C562

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Full id: C562_Smooth_Fibroblast_Preadipocyte_Hepatic_Alveolar_Adipocyte_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:66056544..66056560,-p4@YIF1A
Hg19::chr11:66056564..66056579,-p2@YIF1A
Hg19::chr11:68039364..68039457,-p1@C11orf24
Hg19::chr14:24664776..24664904,-p3@TM9SF1
Hg19::chr19:4670345..4670382,-p1@C19orf10
Hg19::chr1:2323260..2323307,+p1@RER1
Hg19::chr2:220363579..220363641,+p1@GMPPA
Hg19::chr2:27255806..27255879,+p1@TMEM214
Hg19::chr3:10362736..10362809,-p1@SEC13
Hg19::chr3:128968437..128968505,+p1@COPG
Hg19::chr6:33168637..33168704,+p1@SLC39A7
Hg19::chr7:6523755..6523829,-p1@DAGLB
p1@KDELR2
Hg19::chr9:136242894..136242905,-p4@SURF4
Hg19::chr9:136242909..136242953,-p1@SURF4
Hg19::chr9:136242956..136242976,-p2@SURF4
Hg19::chrX:54835499..54835584,+p2@MAGED2


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:0005793ER-Golgi intermediate compartment0.00833926739920197
GO:0000139Golgi membrane0.00833926739920197
GO:0012505endomembrane system0.00833926739920197
GO:0044431Golgi apparatus part0.00833926739920197
GO:0044425membrane part0.0139153532669686
GO:0016192vesicle-mediated transport0.0161922944162981
GO:0031090organelle membrane0.0165749186817612
GO:0005794Golgi apparatus0.0180427800933964
GO:0016021integral to membrane0.0214975997088356
GO:0031224intrinsic to membrane0.0214975997088356
GO:0015031protein transport0.0227785891077271
GO:0005783endoplasmic reticulum0.0227785891077271
GO:0046907intracellular transport0.0227785891077271
GO:0045184establishment of protein localization0.0227785891077271
GO:0008104protein localization0.0227785891077271
GO:0016020membrane0.0227785891077271
GO:0033036macromolecule localization0.0248064161649225
GO:0006890retrograde vesicle-mediated transport, Golgi to ER0.0249997241602398
GO:0051649establishment of cellular localization0.0258787183563686
GO:0030126COPI vesicle coat0.0258787183563686
GO:0030663COPI coated vesicle membrane0.0258787183563686
GO:0051641cellular localization0.0258787183563686
GO:0004806triacylglycerol lipase activity0.0265426724499683
GO:0030137COPI-coated vesicle0.0265426724499683
GO:0006810transport0.0272165256352636
GO:0051234establishment of localization0.0291079438701855
GO:0006829zinc ion transport0.0318924360004973
GO:0005789endoplasmic reticulum membrane0.0368909860600387
GO:0051179localization0.0368909860600387
GO:0042175nuclear envelope-endoplasmic reticulum network0.0369405361170417
GO:0044432endoplasmic reticulum part0.0439203538946573
GO:0006886intracellular protein transport0.0439649120519745



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>

Uber Anatomy
Ontology termp-valuen
trunk mesenchyme3.14e-28143
trunk1.10e-24216
somite1.43e-2383
paraxial mesoderm1.43e-2383
presomitic mesoderm1.43e-2383
presumptive segmental plate1.43e-2383
trunk paraxial mesoderm1.43e-2383
presumptive paraxial mesoderm1.43e-2383
epithelial tube2.48e-23118
unilaminar epithelium2.22e-22138
dermomyotome2.29e-2270
multilaminar epithelium5.34e-2282
skeletal muscle tissue9.74e-2061
striated muscle tissue9.74e-2061
myotome9.74e-2061
mesenchyme1.39e-19238
entire embryonic mesenchyme1.39e-19238
muscle tissue7.89e-1963
musculature7.89e-1963
musculature of body7.89e-1963
vasculature1.45e-1879
vascular system1.45e-1879
splanchnic layer of lateral plate mesoderm1.46e-1784
artery4.30e-1742
arterial blood vessel4.30e-1742
arterial system4.30e-1742
vessel5.90e-1669
blood vessel1.68e-1560
epithelial tube open at both ends1.68e-1560
blood vasculature1.68e-1560
vascular cord1.68e-1560
organism subdivision6.77e-14365
systemic artery1.34e-1333
systemic arterial system1.34e-1333
cardiovascular system1.91e-12110
circulatory system9.08e-12113
mesoderm2.06e-11448
mesoderm-derived structure2.06e-11448
presumptive mesoderm2.06e-11448
multi-tissue structure3.00e-11347
cell layer3.67e-11312
epithelium1.20e-10309
subdivision of trunk2.93e-10113
surface structure1.68e-0995
integument7.57e-0945
integumental system7.57e-0945
multi-cellular organism1.04e-08659
anatomical cluster3.32e-07286
skin of body3.44e-0740
abdominal segment of trunk3.72e-0761
abdomen3.72e-0761
anatomical group4.33e-07626
anatomical system5.50e-07625
aorta7.65e-0721
aortic system7.65e-0721


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#46745.615793631502190.004641412127675220.0219123244373145
BRCA1#67245.046057660805940.006778976696404470.0287730450782649
CCNT2#905124.752151182721972.31381839264867e-071.21985299904005e-05
CHD2#110663.879008562793820.002773171528270150.0151923657805815
CTCFL#14069067.404927884615388.67296992239919e-050.0012991914884186
E2F1#186992.760406433369620.001696428202141060.0105996568952085
E2F4#187453.958768848526390.006382759939409180.0277846392677541
E2F6#1876134.076439032004132.37289564027328e-071.2459670576898e-05
EBF1#187973.896579245373940.001021158414795670.00724368428192929
ELF1#1997153.991966836382074.54061180224701e-093.66757119887761e-07
ELK4#20051111.16203114019681.57457980886855e-101.65941009746137e-08
ESR1#209935.769113118028970.01399042242294870.0491157930495255
ETS1#2113159.120713364564692.17334805334434e-143.66100479585854e-12
GABPB1#2553125.300762877136636.68540345520611e-084.06886277073585e-06
HEY1#23462164.040111043105711.98084199021544e-102.05031869788018e-08
HMGN3#932484.08927386167530.0002572852935955120.00276816923640896
IRF1#3659115.250550080575184.46896063357945e-072.12731895902645e-05
JUND#3727114.808831460036331.10371712893257e-064.57788376602813e-05
MAX#414993.629562473816510.0002071788170627830.00243501558352689
MXI1#460195.60338404117716.10807177715345e-060.000181640349753454
MYC#4609134.243104020682641.44725283711898e-078.17909302250373e-06
NFKB1#479082.744031712096920.003856163139355890.0190246975346587
NFYA#480044.606395174957630.009320267223685850.0352055911090646
NFYB#480177.33240954842221.90141463325496e-050.000430669795884872
NRF1#489986.105139723855451.42402144556288e-050.00034063988949414
PAX5#5079125.002174148383371.2934425150475e-077.37770851059781e-06
POLR2A#5430162.147453176558074.88536678567824e-060.000151042872033585
POU2F2#5452105.691327536089081.08661015877248e-064.51589647322081e-05
REST#597874.221887563306010.0006272813656043830.0051633542356838
RXRA#625645.018654284783320.006909951752017850.0292576198422522
SIN3A#25942155.070829431389191.3297899225369e-101.42297059139172e-08
SIX5#14791299.611277387445696.29588488815385e-083.88614611012943e-06
SP1#6667134.629934869739484.9106978951726e-083.16195053929674e-06
SPI1#668894.614931973544033.01826774164688e-050.000620643561074736
SRF#672286.89858913108395.75315050227476e-060.000172857677015844
TAF1#6872153.134105892886211.57946317760101e-078.84016906781733e-06
TAF7#687975.001967864654210.0002195065578727680.00248752662735178
TBP#6908153.475097519152863.48271765686805e-082.32564929261919e-06
TCF12#693863.987924338319910.002406057678715160.0135669073484144
TCF7L2#693464.03881621117650.002254045226455730.0128037762104759
THAP1#55145611.76342922606926.36151165140569e-060.000187627764857712
YY1#7528133.990326234256263.08644499595592e-071.54973667756077e-05
ZNF263#1012763.0831906138790.008734686727107120.0331832944269885



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.

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