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Coexpression cluster:C345: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C345_Mesenchymal_Fibroblast_Alveolar_Renal_Pericytes_Hepatic_Smooth
|full_id=C345_Mesenchymal_Fibroblast_Alveolar_Renal_Pericytes_Hepatic_Smooth
|gostat_on_coexpression_clusters=GO:0008283!cell proliferation!0.0340738507394172!3611;826;7041;706;1489$GO:0005515!protein binding!0.0340738507394172!682;5605;6576;1489;3611;57175;11344;826;30846;10489;4350;392;10945;7041;5589;59$GO:0042127!regulation of cell proliferation!0.0340738507394172!3611;826;7041;1489$GO:0006839!mitochondrial transport!0.0340738507394172!6576;706$GO:0016798!hydrolase activity, acting on glycosyl bonds!0.0340738507394172!5589;4350;55741$GO:0006843!mitochondrial citrate transport!0.0340738507394172!6576$GO:0008284!positive regulation of cell proliferation!0.0340738507394172!3611;826;1489$GO:0005509!calcium ion binding!0.0340738507394172!826;5589;30846;57048;6284;55741$GO:0015746!citrate transport!0.0340738507394172!6576$GO:0006842!tricarboxylic acid transport!0.0340738507394172!6576$GO:0032374!regulation of cholesterol transport!0.0340738507394172!706$GO:0015137!citrate transmembrane transporter activity!0.0340738507394172!6576$GO:0005046!KDEL sequence binding!0.0340738507394172!10945$GO:0032371!regulation of sterol transport!0.0340738507394172!706$GO:0005146!leukemia inhibitory factor receptor binding!0.0340738507394172!1489$GO:0032368!regulation of lipid transport!0.0340738507394172!706$GO:0017177!alpha-glucosidase II complex!0.0340738507394172!5589$GO:0015142!tricarboxylic acid transmembrane transporter activity!0.0340738507394172!6576$GO:0005886!plasma membrane!0.0404754078722562!6237;826;682;30846;392;7041;3611;57048;11344$GO:0007005!mitochondrion organization and biogenesis!0.0418019066043096!6576;706$GO:0003905!alkylbase DNA N-glycosylase activity!0.0418019066043096!4350$GO:0006307!DNA dealkylation!0.0418019066043096!4350$GO:0046943!carboxylic acid transmembrane transporter activity!0.0452564800025801!6576;8273$GO:0005342!organic acid transmembrane transporter activity!0.0452564800025801!6576;8273$GO:0016043!cellular component organization and biogenesis!0.0453970416460283!3611;55766;30846;57048;392;6576;10945;706$GO:0017121!phospholipid scrambling!0.0453970416460283!57048$GO:0017128!phospholipid scramblase activity!0.0453970416460283!57048
|gostat_on_coexpression_clusters=GO:0008283!cell proliferation!0.0340738507394172!3611;826;7041;706;1489$GO:0005515!protein binding!0.0340738507394172!682;5605;6576;1489;3611;57175;11344;826;30846;10489;4350;392;10945;7041;5589;59$GO:0042127!regulation of cell proliferation!0.0340738507394172!3611;826;7041;1489$GO:0006839!mitochondrial transport!0.0340738507394172!6576;706$GO:0016798!hydrolase activity, acting on glycosyl bonds!0.0340738507394172!5589;4350;55741$GO:0006843!mitochondrial citrate transport!0.0340738507394172!6576$GO:0008284!positive regulation of cell proliferation!0.0340738507394172!3611;826;1489$GO:0005509!calcium ion binding!0.0340738507394172!826;5589;30846;57048;6284;55741$GO:0015746!citrate transport!0.0340738507394172!6576$GO:0006842!tricarboxylic acid transport!0.0340738507394172!6576$GO:0032374!regulation of cholesterol transport!0.0340738507394172!706$GO:0015137!citrate transmembrane transporter activity!0.0340738507394172!6576$GO:0005046!KDEL sequence binding!0.0340738507394172!10945$GO:0032371!regulation of sterol transport!0.0340738507394172!706$GO:0005146!leukemia inhibitory factor receptor binding!0.0340738507394172!1489$GO:0032368!regulation of lipid transport!0.0340738507394172!706$GO:0017177!alpha-glucosidase II complex!0.0340738507394172!5589$GO:0015142!tricarboxylic acid transmembrane transporter activity!0.0340738507394172!6576$GO:0005886!plasma membrane!0.0404754078722562!6237;826;682;30846;392;7041;3611;57048;11344$GO:0007005!mitochondrion organization and biogenesis!0.0418019066043096!6576;706$GO:0003905!alkylbase DNA N-glycosylase activity!0.0418019066043096!4350$GO:0006307!DNA dealkylation!0.0418019066043096!4350$GO:0046943!carboxylic acid transmembrane transporter activity!0.0452564800025801!6576;8273$GO:0005342!organic acid transmembrane transporter activity!0.0452564800025801!6576;8273$GO:0016043!cellular component organization and biogenesis!0.0453970416460283!3611;55766;30846;57048;392;6576;10945;706$GO:0017121!phospholipid scrambling!0.0453970416460283!57048$GO:0017128!phospholipid scramblase activity!0.0453970416460283!57048

Revision as of 16:23, 12 September 2012


Full id: C345_Mesenchymal_Fibroblast_Alveolar_Renal_Pericytes_Hepatic_Smooth



Phase1 CAGE Peaks

Hg19::chr10:90751038..90751131,-p2@ACTA2
Hg19::chr10:99258760..99258810,+p2@UBTD1
Hg19::chr11:46722117..46722183,-p1@ARHGAP1
Hg19::chr11:6624970..6625034,+p1@ILK
Hg19::chr11:66313492..66313546,-p1@ZDHHC24
Hg19::chr11:67210930..67210974,-p1@CORO1B
Hg19::chr12:14927297..14927347,+p1@H2AFJ
Hg19::chr12:58120044..58120095,+p1@ENST00000542466
Hg19::chr12:6875684..6875720,+p2@PTMS
Hg19::chr16:128201..128270,+p1@MPG
Hg19::chr16:128274..128286,+p2@MPG
Hg19::chr16:30905269..30905292,-p3@BCL7C
Hg19::chr16:30907927..30907963,+p1@CTF1
Hg19::chr16:31483451..31483507,+p1@TGFB1I1
Hg19::chr17:7297833..7297871,-p2@PLSCR3
Hg19::chr19:11546443..11546485,+p1@PRKCSH
Hg19::chr19:36630961..36631044,+p1@CAPNS1
Hg19::chr19:4124079..4124128,-p1@MAP2K2
Hg19::chr19:48216669..48216685,+p1@EHD2
Hg19::chr19:48894762..48894830,-p1@KDELR1
Hg19::chr19:50143268..50143279,-p3@RRAS
Hg19::chr19:50143346..50143409,-p1@RRAS
Hg19::chr19:51014403..51014420,-p3@JOSD2
Hg19::chr19:572543..572579,+p2@BSG
Hg19::chr1:153599994..153600045,-p2@S100A13
Hg19::chr1:46768851..46768867,-p2@LRRC41
Hg19::chr20:33865891..33865939,-p1@EDEM2
p1@MT1P3
Hg19::chr22:19165917..19166026,-p3@SLC25A1
Hg19::chr22:43547533..43547590,+p1@TSPO
Hg19::chr22:50946114..50946140,-p1@LMF2
Hg19::chr3:52273098..52273181,-p1@TWF2
Hg19::chrX:153718988..153719008,-p2@SLC10A3


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:0008283cell proliferation0.0340738507394172
GO:0005515protein binding0.0340738507394172
GO:0042127regulation of cell proliferation0.0340738507394172
GO:0006839mitochondrial transport0.0340738507394172
GO:0016798hydrolase activity, acting on glycosyl bonds0.0340738507394172
GO:0006843mitochondrial citrate transport0.0340738507394172
GO:0008284positive regulation of cell proliferation0.0340738507394172
GO:0005509calcium ion binding0.0340738507394172
GO:0015746citrate transport0.0340738507394172
GO:0006842tricarboxylic acid transport0.0340738507394172
GO:0032374regulation of cholesterol transport0.0340738507394172
GO:0015137citrate transmembrane transporter activity0.0340738507394172
GO:0005046KDEL sequence binding0.0340738507394172
GO:0032371regulation of sterol transport0.0340738507394172
GO:0005146leukemia inhibitory factor receptor binding0.0340738507394172
GO:0032368regulation of lipid transport0.0340738507394172
GO:0017177alpha-glucosidase II complex0.0340738507394172
GO:0015142tricarboxylic acid transmembrane transporter activity0.0340738507394172
GO:0005886plasma membrane0.0404754078722562
GO:0007005mitochondrion organization and biogenesis0.0418019066043096
GO:0003905alkylbase DNA N-glycosylase activity0.0418019066043096
GO:0006307DNA dealkylation0.0418019066043096
GO:0046943carboxylic acid transmembrane transporter activity0.0452564800025801
GO:0005342organic acid transmembrane transporter activity0.0452564800025801
GO:0016043cellular component organization and biogenesis0.0453970416460283
GO:0017121phospholipid scrambling0.0453970416460283
GO:0017128phospholipid scramblase activity0.0453970416460283



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
somite5.55e-2583
paraxial mesoderm5.55e-2583
presomitic mesoderm5.55e-2583
presumptive segmental plate5.55e-2583
trunk paraxial mesoderm5.55e-2583
presumptive paraxial mesoderm5.55e-2583
vasculature8.70e-2579
vascular system8.70e-2579
multilaminar epithelium4.55e-2482
splanchnic layer of lateral plate mesoderm5.76e-2484
trunk mesenchyme8.66e-24143
dermomyotome5.07e-2370
trunk6.72e-22216
epithelial tube8.00e-22118
vessel2.34e-2169
blood vessel1.43e-2060
epithelial tube open at both ends1.43e-2060
blood vasculature1.43e-2060
vascular cord1.43e-2060
skeletal muscle tissue3.36e-2061
striated muscle tissue3.36e-2061
myotome3.36e-2061
muscle tissue1.02e-1963
musculature1.02e-1963
musculature of body1.02e-1963
cardiovascular system1.80e-19110
circulatory system2.36e-19113
artery5.28e-1842
arterial blood vessel5.28e-1842
arterial system5.28e-1842
unilaminar epithelium6.92e-17138
mesenchyme2.19e-16238
entire embryonic mesenchyme2.19e-16238
organism subdivision2.46e-16365
multi-cellular organism3.02e-16659
cell layer9.37e-15312
epithelium2.55e-14309
systemic artery3.35e-1433
systemic arterial system3.35e-1433
mesoderm7.22e-14448
mesoderm-derived structure7.22e-14448
presumptive mesoderm7.22e-14448
multi-tissue structure1.60e-13347
anatomical system2.74e-13625
anatomical group4.51e-13626
anatomical cluster2.06e-10286
surface structure5.61e-1095
embryonic structure6.66e-10605
developing anatomical structure6.66e-10605
germ layer8.29e-10604
embryonic tissue8.29e-10604
presumptive structure8.29e-10604
epiblast (generic)8.29e-10604
embryo2.37e-09612
compound organ8.43e-0969
anatomical conduit2.15e-08241
aorta3.29e-0821
aortic system3.29e-0821
integument3.58e-0745
integumental system3.58e-0745
subdivision of trunk6.92e-07113
nephron epithelium7.44e-0716
nephron7.44e-0716
uriniferous tubule7.44e-0716
metanephric mesenchyme7.44e-0716
nephrogenic mesenchyme7.44e-0716


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
CCNT2#905193.762119686321562.45529810576708e-081.71524333691109e-06
CTCF#10664122.010096139903140.009693455350319310.0364740878848537
E2F1#1869192.91376234633461.59993879657804e-066.080640756034e-05
E2F4#187483.167015078821110.002824061070448750.0154549420528504
E2F6#1876152.351791749233150.0005393272461342730.00465934306055235
EGR1#1958213.273492530969152.7582276701744e-081.89020039137365e-06
ELF1#1997202.661311224254712.85023666346111e-069.80810105091318e-05
ETS1#211392.736214009369410.003964869419353730.0190297333312447
GABPB1#2553132.871246558449010.0002222924278741460.00247690161898517
GATA1#262372.966317406456350.007717067986545590.0317633350455914
GTF2F1#296272.786800816790740.01072851154934940.0395983537497349
HEY1#23462263.282590222523393.02301702543147e-113.50023143147492e-09
HMGN3#9324174.344853478032.74478412909867e-081.8822226504198e-06
IRF1#3659163.818581876781955.50305036801123e-072.54870544294778e-05
MAX#4149132.621350675534140.0005542060441926070.00473113659060256
MXI1#4601134.046888474183465.73151353453395e-060.000172405974087901
MYC#4609162.61114093580478.34241073906737e-050.00125290916764086
NFKB1#4790183.087035676109031.64350787647976e-066.2258367468868e-05
NRF1#4899103.815712327409660.0001615170890580470.00201033050460415
PAX5#5079122.501087074191690.001529267915847630.009736951281059
PBX3#509053.424142607303770.01421510919864690.049862691932474
POLR2A#5430322.147453176558072.38288969218142e-112.82802973365608e-09
POU2F2#545292.561097391240080.00615271311541260.0272004404444876
RAD21#588582.588758473864080.009543692067054940.0359429395186308
SIN3A#25942193.211525306546493.34308292587877e-071.66261065569454e-05
SIX5#14791263.203759129148560.009743065837533320.0366383196992094
SMARCB1#659873.992781577128180.00147741614525670.0094511738818121
SMC3#912683.761233211233210.0009415686277859290.00681519758246133
SP1#6667162.849190689070452.75078925299075e-050.000584992219085931
TAF1#6872272.820695303597592.58522491432065e-102.63927961707463e-08
TAF7#687993.215550770134850.001299643352260150.00870700186456465
TBP#6908232.664241431350531.56369160124714e-078.7565891229303e-06
TFAP2A#702063.097243944945930.01140183021635940.0417779092013597
TFAP2C#702293.040095546523190.001927586587780460.011328937289882
THAP1#5514565.881714613034620.0004645265748502270.00427555221210742
USF1#7391173.379546491016731.11830647159922e-064.60365824151956e-05
USF2#739293.654055514550820.0005172598164098650.00448204579490831
XRCC4#75181134.3219476744190.007418635500041630.0306388355341999
YY1#7528152.302111288993990.0006839964643864990.00551671223600753
ZBTB7A#51341184.135448985680191.73869450393486e-081.25666100551179e-06
ZNF143#7702104.219023922571226.97820471448877e-050.00110608092605326
ZNF263#10127112.826258062722420.0009518015016662430.00685269523180206



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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