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Coexpression cluster:C345: Difference between revisions

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{{Coexpression_clusters
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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 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.907598,0.936275,0.727813,0.379326,0.875874,0.150181,0.962206,0.778444,0.557127,0.705174,0.906526,0.698421,0.943743,0.603633,0.73098,0.927463,0.286521,0.729232,0.672247,0.895731,0.469752,0.474507,0.367991,0.571578,0.933372,0.281892,0.924135,0.513504,0.239135,0.658728,0.616475,0.982832,0.8659,0.281494,0.436293,0.544718,0.849223,0.678885,0.931789,0.873062,0.544621,0.731004,0.95533,0.914555,0.951645|tfbs_overrepresentation_for_novel_motifs=1.03156,1.9414,1.42551,0.0978295,0.0282624,0.0970322,0.839768,0.405405,0.622136,3.66696,0.282316,0.16234,1.56848,0.408634,0.116409,0.0341629,1.41238,0.0163503,0.306745,0.510681,0.0400195,0.696425,1.5826,0.273486,0.781611,0.176305,0.113263,0.307965,1.65812,0.938789,0.543916,0.310643,1.87584,0.93913,0.700235,0.281297,2.3134,0.662617,0.184446,1.81185,0.0886746,1.3165,0.126382,0.0275386,4.3963,0.187401,1.36185,0.268937,0.0263459,0.845824,0.544488,0.443561,0.311481,0.968932,0.497309,0.818987,0.0301877,1.21497,0.689285,0.738352,0.906297,1.37014,0.106768,0.727251,0.455994,1.24683,0.574343,0.913986,0.302792,0.761456,1.757,0.115641,3.25232,0.495593,2.73673,1.40579,0.0998,0.250834,0.300348,0.0532365,0.0261516,0.725474,0.149063,0.00746868,0.451923,11.9864,0.0297081,1.49334,1.10675,1.00897,0.65804,1.0976,0.323471,0.0587302,0.283574,0.0669363,0.164811,0.356655,0.20516,0.566574,0.015471,0.854854,0.352258,0.285815,0.230532,2.0146,1.37969,0.128645,0.203318,1.99911,0.67607,0.350081,0.150691,1.02782,0.614737,0.217377,4.01639,0.92153,1.92561,0.0125651,0.488501,0.200525,0.0957026,0.47206,0.715288,0.251373,0.133408,0.327313,0.525232,2.06222,0.429962,0.0746108,0.537753,0.153736,0.669744,0.851717,0.0708821,0.0925536,0.631317,1.45283,1.05945,0.597865,0.134374,0.353873,0.231743,0.110137,0.220337,1.29622,0.0653198,0.523233,1.57678,6.1987,0.430278,1.16202,0.138651,0.789951,0.191579,0.024864,0.0554952,3.1805,0.596781,0.414981,0.299757,0.397308,0.242939,0.454322,0.48192,0.13622,4.55089|tfbs_overrepresentation_jaspar=MA0003.1;9.14562,MA0004.1;1.01395,MA0006.1;0.825963,MA0007.1;0.561709,MA0009.1;1.02469,MA0014.1;9.73641,MA0017.1;0.631118,MA0019.1;0.165418,MA0024.1;0.840207,MA0025.1;0.508683,MA0027.1;1.93196,MA0028.1;3.37058,MA0029.1;0.327543,MA0030.1;0.318663,MA0031.1;0.270046,MA0038.1;0.429002,MA0040.1;0.332103,MA0041.1;0.0940493,MA0042.1;0.0792314,MA0043.1;0.39615,MA0046.1;0.386991,MA0048.1;1.47574,MA0050.1;0.273123,MA0051.1;0.836165,MA0052.1;0.335128,MA0055.1;1.02477,MA0056.1;0,MA0057.1;2.43783,MA0058.1;0.707343,MA0059.1;1.53355,MA0060.1;0.623774,MA0061.1;1.7167,MA0063.1;0,MA0066.1;0.138793,MA0067.1;0.673046,MA0068.1;0.0455946,MA0069.1;0.383853,MA0070.1;0.374777,MA0071.1;0.1171,MA0072.1;0.371146,MA0073.1;2.26088,MA0074.1;1.95193,MA0076.1;1.62713,MA0077.1;0.364942,MA0078.1;0.197204,MA0081.1;0.397764,MA0083.1;0.40206,MA0084.1;0.847335,MA0087.1;0.369175,MA0088.1;2.14683,MA0089.1;0,MA0090.1;0.210825,MA0091.1;0.0865076,MA0092.1;0.245507,MA0093.1;1.2136,MA0095.1;0,MA0098.1;0,MA0100.1;0.146599,MA0101.1;0.851211,MA0103.1;0.263087,MA0105.1;5.8192,MA0106.1;0.949623,MA0107.1;1.20036,MA0108.2;0.738478,MA0109.1;0,MA0111.1;0.226279,MA0113.1;0.173209,MA0114.1;0.833833,MA0115.1;0.603788,MA0116.1;3.06137,MA0117.1;1.09244,MA0119.1;0.36594,MA0122.1;0.44876,MA0124.1;0.566745,MA0125.1;0.493194,MA0130.1;0,MA0131.1;1.13481,MA0132.1;0,MA0133.1;0,MA0135.1;0.420972,MA0136.1;0.439289,MA0139.1;2.83902,MA0140.1;0.115685,MA0141.1;0.698058,MA0142.1;0.247045,MA0143.1;0.173319,MA0144.1;0.765659,MA0145.1;1.16026,MA0146.1;5.94791,MA0147.1;1.644,MA0148.1;0.321092,MA0149.1;0.110599,MA0062.2;2.94188,MA0035.2;0.11531,MA0039.2;24.1262,MA0138.2;0.575161,MA0002.2;0.0316769,MA0137.2;0.581971,MA0104.2;1.21494,MA0047.2;0.155654,MA0112.2;2.9632,MA0065.2;1.46576,MA0150.1;0.0556869,MA0151.1;0,MA0152.1;0.119196,MA0153.1;0.478697,MA0154.1;1.51433,MA0155.1;2.46092,MA0156.1;0.588601,MA0157.1;0.227782,MA0158.1;0,MA0159.1;1.24747,MA0160.1;0.341393,MA0161.1;0,MA0162.1;8.18353,MA0163.1;4.05737,MA0164.1;0.181076,MA0080.2;0.11873,MA0018.2;0.163878,MA0099.2;0.119388,MA0079.2;25.7815,MA0102.2;0.88257,MA0258.1;0.272176,MA0259.1;0.933859,MA0442.1;0}}
|full_id=C345_Mesenchymal_Fibroblast_Alveolar_Renal_Pericytes_Hepatic_Smooth
|id=C345
}}

Latest revision as of 11:20, 17 September 2013


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
epithelial vesicle5.95e-2678
vasculature1.58e-2478
vascular system1.58e-2478
splanchnic layer of lateral plate mesoderm2.61e-2383
multilaminar epithelium4.25e-2383
somite1.57e-2271
presomitic mesoderm1.57e-2271
presumptive segmental plate1.57e-2271
dermomyotome1.57e-2271
trunk paraxial mesoderm1.57e-2271
dense mesenchyme tissue3.35e-2273
paraxial mesoderm7.11e-2272
presumptive paraxial mesoderm7.11e-2272
epithelial tube1.22e-21117
vessel3.17e-2168
mesenchyme6.04e-21160
entire embryonic mesenchyme6.04e-21160
epithelial tube open at both ends4.18e-2059
blood vessel4.18e-2059
blood vasculature4.18e-2059
vascular cord4.18e-2059
organism subdivision5.17e-20264
cardiovascular system7.58e-20109
skeletal muscle tissue8.03e-2062
striated muscle tissue8.03e-2062
myotome8.03e-2062
circulatory system1.15e-19112
muscle tissue3.60e-1964
musculature3.60e-1964
musculature of body3.60e-1964
unilaminar epithelium4.91e-19148
trunk1.88e-18199
trunk mesenchyme2.55e-18122
artery3.40e-1842
arterial blood vessel3.40e-1842
arterial system3.40e-1842
systemic artery3.66e-1433
systemic arterial system3.66e-1433
mesoderm4.52e-14315
mesoderm-derived structure4.52e-14315
presumptive mesoderm4.52e-14315
multi-cellular organism7.02e-13656
cell layer8.75e-12309
anatomical system1.25e-11624
anatomical group1.67e-11625
epithelium2.00e-11306
surface structure1.45e-0999
multi-tissue structure3.75e-09342
compound organ3.06e-0868
aorta4.40e-0821
aortic system4.40e-0821
integument2.99e-0746
integumental system2.99e-0746
nephron epithelium6.17e-0715
renal tubule6.17e-0715
nephron tubule6.17e-0715
nephron6.17e-0715
uriniferous tubule6.17e-0715
nephrogenic mesenchyme6.17e-0715
developing anatomical structure6.40e-07581
excretory tube6.85e-0716
kidney epithelium6.85e-0716
urinary system structure9.61e-0747


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)
MA0003.19.14562
MA0004.11.01395
MA0006.10.825963
MA0007.10.561709
MA0009.11.02469
MA0014.19.73641
MA0017.10.631118
MA0019.10.165418
MA0024.10.840207
MA0025.10.508683
MA0027.11.93196
MA0028.13.37058
MA0029.10.327543
MA0030.10.318663
MA0031.10.270046
MA0038.10.429002
MA0040.10.332103
MA0041.10.0940493
MA0042.10.0792314
MA0043.10.39615
MA0046.10.386991
MA0048.11.47574
MA0050.10.273123
MA0051.10.836165
MA0052.10.335128
MA0055.11.02477
MA0056.10
MA0057.12.43783
MA0058.10.707343
MA0059.11.53355
MA0060.10.623774
MA0061.11.7167
MA0063.10
MA0066.10.138793
MA0067.10.673046
MA0068.10.0455946
MA0069.10.383853
MA0070.10.374777
MA0071.10.1171
MA0072.10.371146
MA0073.12.26088
MA0074.11.95193
MA0076.11.62713
MA0077.10.364942
MA0078.10.197204
MA0081.10.397764
MA0083.10.40206
MA0084.10.847335
MA0087.10.369175
MA0088.12.14683
MA0089.10
MA0090.10.210825
MA0091.10.0865076
MA0092.10.245507
MA0093.11.2136
MA0095.10
MA0098.10
MA0100.10.146599
MA0101.10.851211
MA0103.10.263087
MA0105.15.8192
MA0106.10.949623
MA0107.11.20036
MA0108.20.738478
MA0109.10
MA0111.10.226279
MA0113.10.173209
MA0114.10.833833
MA0115.10.603788
MA0116.13.06137
MA0117.11.09244
MA0119.10.36594
MA0122.10.44876
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.11.13481
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.439289
MA0139.12.83902
MA0140.10.115685
MA0141.10.698058
MA0142.10.247045
MA0143.10.173319
MA0144.10.765659
MA0145.11.16026
MA0146.15.94791
MA0147.11.644
MA0148.10.321092
MA0149.10.110599
MA0062.22.94188
MA0035.20.11531
MA0039.224.1262
MA0138.20.575161
MA0002.20.0316769
MA0137.20.581971
MA0104.21.21494
MA0047.20.155654
MA0112.22.9632
MA0065.21.46576
MA0150.10.0556869
MA0151.10
MA0152.10.119196
MA0153.10.478697
MA0154.11.51433
MA0155.12.46092
MA0156.10.588601
MA0157.10.227782
MA0158.10
MA0159.11.24747
MA0160.10.341393
MA0161.10
MA0162.18.18353
MA0163.14.05737
MA0164.10.181076
MA0080.20.11873
MA0018.20.163878
MA0099.20.119388
MA0079.225.7815
MA0102.20.88257
MA0258.10.272176
MA0259.10.933859
MA0442.10



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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