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{{Coexpression_clusters
{
|full_id=C385_Mesenchymal_Alveolar_Osteoblast_Smooth_Renal_Placental_Fibroblast
|

Latest revision as of 11:21, 17 September 2013


Full id: C385_Mesenchymal_Alveolar_Osteoblast_Smooth_Renal_Placental_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:129903123..129903147,-p1@TCEB2P2
Hg19::chr11:63993738..63993778,+p1@NUDT22
Hg19::chr11:64052114..64052210,-p1@BAD
Hg19::chr11:64085563..64085736,+p1@PRDX5
Hg19::chr11:6633406..6633456,-p1@TAF10
Hg19::chr14:94595896..94595949,-p1@IFI27L2
Hg19::chr15:44084503..44084563,+p1@SERF2
Hg19::chr16:1401799..1401896,-p1@C16orf42
Hg19::chr16:2827261..2827299,-p1@TCEB2
Hg19::chr16:30905311..30905428,-p1@BCL7C
Hg19::chr17:3571887..3571918,-p2@TAX1BP3
Hg19::chr17:79849591..79849644,+p1@ANAPC11
Hg19::chr19:14682838..14682894,-p1@NDUFB7
Hg19::chr19:17622415..17622481,+p1@PGLS
Hg19::chr19:19030157..19030210,-p1@COPE
Hg19::chr19:4124133..4124149,-p2@MAP2K2
Hg19::chr19:51014430..51014455,-p2@JOSD2
Hg19::chr19:51014460..51014503,-p1@JOSD2
Hg19::chr19:7745708..7745752,+p1@TRAPPC5
Hg19::chr22:20307537..20307590,-p1@DGCR6L
Hg19::chr22:41985798..41985852,-p1@PMM1
Hg19::chr3:49395773..49395819,-p1@GPX1
Hg19::chr3:9834088..9834176,-p1@TADA3
Hg19::chr7:100861427..100861471,+p1@ZNHIT1
Hg19::chr7:100888337..100888377,-p1@FIS1
Hg19::chr7:100888385..100888396,-p3@FIS1
Hg19::chr9:139743853..139743878,+p1@PHPT1
Hg19::chr9:140446314..140446398,+p1@MRPL41


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:0005739mitochondrion0.00620645344517677
GO:0005737cytoplasm0.00761501180775182
GO:0044444cytoplasmic part0.00761501180775182
GO:0006915apoptosis0.00761501180775182
GO:0012501programmed cell death0.00761501180775182
GO:0016265death0.00761501180775182
GO:0008219cell death0.00761501180775182
GO:0043231intracellular membrane-bound organelle0.00772619952853591
GO:0043227membrane-bound organelle0.00772619952853591
GO:0044429mitochondrial part0.012211775933763
GO:0010269response to selenium ion0.0180924827404877
GO:0048468cell development0.0180924827404877
GO:0004601peroxidase activity0.0180924827404877
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0180924827404877
GO:0005741mitochondrial outer membrane0.019637546591411
GO:0033598mammary gland epithelial cell proliferation0.019637546591411
GO:0008539proteasome inhibitor activity0.019637546591411
GO:0033599regulation of mammary gland epithelial cell proliferation0.019637546591411
GO:0008969phosphohistidine phosphatase activity0.019637546591411
GO:0008632apoptotic program0.019637546591411
GO:0007005mitochondrion organization and biogenesis0.019637546591411
GO:0031968organelle outer membrane0.019637546591411
GO:0019867outer membrane0.019637546591411
GO:0044424intracellular part0.019637546591411
GO:0042579microbody0.019637546591411
GO:0005777peroxisome0.019637546591411
GO:0031966mitochondrial membrane0.019637546591411
GO:0043295glutathione binding0.019637546591411
GO:00170576-phosphogluconolactonase activity0.019637546591411
GO:0000266mitochondrial fission0.019637546591411
GO:0019307mannose biosynthetic process0.019637546591411
GO:0004615phosphomannomutase activity0.019637546591411
GO:0005740mitochondrial envelope0.021381196836168
GO:0006979response to oxidative stress0.0226387669961546
GO:0044455mitochondrial membrane part0.0226387669961546
GO:0008631induction of apoptosis by oxidative stress0.0226387669961546
GO:0031307integral to mitochondrial outer membrane0.0226387669961546
GO:0031306intrinsic to mitochondrial outer membrane0.0272464569702817
GO:0043229intracellular organelle0.0272464569702817
GO:0043226organelle0.0272464569702817
GO:0048869cellular developmental process0.0272988937719487
GO:0030154cell differentiation0.0272988937719487
GO:0009650UV protection0.0272988937719487
GO:0016559peroxisome fission0.0272988937719487
GO:0051920peroxiredoxin activity0.0272988937719487
GO:0032592integral to mitochondrial membrane0.0272988937719487
GO:0048285organelle fission0.034862420969153
GO:0030503regulation of cell redox homeostasis0.034862420969153
GO:0043154negative regulation of caspase activity0.0384090722914862
GO:0031967organelle envelope0.0388818993684594
GO:0031975envelope0.0388818993684594
GO:0006368RNA elongation from RNA polymerase II promoter0.0402033875658268
GO:0006917induction of apoptosis0.0431027183745183
GO:0012502induction of programmed cell death0.0431027183745183
GO:0006890retrograde vesicle-mediated transport, Golgi to ER0.0431027183745183
GO:0042744hydrogen peroxide catabolic process0.0431027183745183
GO:0044446intracellular organelle part0.0431027183745183
GO:0044422organelle part0.0431027183745183
GO:0005794Golgi apparatus0.0431027183745183
GO:0001836release of cytochrome c from mitochondria0.0431027183745183
GO:0006740NADPH regeneration0.0431027183745183
GO:0006098pentose-phosphate shunt0.0431027183745183
GO:0042743hydrogen peroxide metabolic process0.0431027183745183
GO:0005515protein binding0.0443883691234917
GO:0006013mannose metabolic process0.0443883691234917
GO:0005762mitochondrial large ribosomal subunit0.0443883691234917
GO:0030663COPI coated vesicle membrane0.0443883691234917
GO:0000315organellar large ribosomal subunit0.0443883691234917
GO:0030126COPI vesicle coat0.0443883691234917
GO:0005779integral to peroxisomal membrane0.0443883691234917
GO:0031231intrinsic to peroxisomal membrane0.0443883691234917
GO:0004602glutathione peroxidase activity0.0443883691234917
GO:0065003macromolecular complex assembly0.0443883691234917
GO:0043065positive regulation of apoptosis0.0443883691234917
GO:0005622intracellular0.0443883691234917
GO:0006891intra-Golgi vesicle-mediated transport0.0443883691234917
GO:0030137COPI-coated vesicle0.0443883691234917
GO:0006739NADP metabolic process0.0443883691234917
GO:0005680anaphase-promoting complex0.0443883691234917
GO:0043068positive regulation of programmed cell death0.0443883691234917
GO:0030178negative regulation of Wnt receptor signaling pathway0.0457598392455279
GO:0006354RNA elongation0.0457598392455279
GO:0031090organelle membrane0.0457598392455279
GO:0019318hexose metabolic process0.0457863884821124
GO:0006749glutathione metabolic process0.0457888876222452
GO:0008637apoptotic mitochondrial changes0.0457888876222452
GO:0005996monosaccharide metabolic process0.0457888876222452
GO:0022607cellular component assembly0.0463276222825077
GO:0042542response to hydrogen peroxide0.0463276222825077
GO:0017124SH3 domain binding0.0463276222825077
GO:0000152nuclear ubiquitin ligase complex0.0476122033922862
GO:0006732coenzyme metabolic process0.0476122033922862



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 vesicle2.39e-2578
multilaminar epithelium2.15e-2283
dense mesenchyme tissue3.67e-2273
somite3.74e-2271
presomitic mesoderm3.74e-2271
presumptive segmental plate3.74e-2271
dermomyotome3.74e-2271
trunk paraxial mesoderm3.74e-2271
paraxial mesoderm9.24e-2272
presumptive paraxial mesoderm9.24e-2272
skeletal muscle tissue1.01e-1962
striated muscle tissue1.01e-1962
myotome1.01e-1962
muscle tissue1.58e-1864
musculature1.58e-1864
musculature of body1.58e-1864
unilaminar epithelium5.75e-18148
mesenchyme2.89e-17160
entire embryonic mesenchyme2.89e-17160
organism subdivision6.36e-17264
trunk mesenchyme6.49e-17122
splanchnic layer of lateral plate mesoderm1.04e-1583
vasculature1.65e-1578
vascular system1.65e-1578
epithelial tube1.98e-15117
trunk2.75e-15199
epithelial tube open at both ends3.72e-1359
blood vessel3.72e-1359
blood vasculature3.72e-1359
vascular cord3.72e-1359
circulatory system3.84e-13112
artery4.75e-1342
arterial blood vessel4.75e-1342
arterial system4.75e-1342
vessel6.60e-1368
cardiovascular system1.94e-12109
epithelium2.55e-12306
cell layer2.96e-12309
multi-tissue structure1.07e-10342
systemic artery1.79e-0933
systemic arterial system1.79e-0933
compound organ2.85e-0768
mesoderm4.12e-07315
mesoderm-derived structure4.12e-07315
presumptive mesoderm4.12e-07315
anatomical cluster4.89e-07373


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)
MA0003.17.12749
MA0004.11.72157
MA0006.11.4238
MA0007.10.668837
MA0009.10.441048
MA0014.17.0918
MA0017.10.0536635
MA0019.10.197704
MA0024.10.354374
MA0025.10.557187
MA0027.11.98963
MA0028.17.59223
MA0029.10.369985
MA0030.10.360703
MA0031.10.309631
MA0038.10.168286
MA0040.10.374747
MA0041.10.11856
MA0042.10.10161
MA0043.10.441316
MA0046.10.431829
MA0048.10.672202
MA0050.10.102063
MA0051.10.165625
MA0052.10.377904
MA0055.11.17568
MA0056.10
MA0057.10.279644
MA0058.12.9692
MA0059.11.77994
MA0060.12.87119
MA0061.10.950362
MA0063.10
MA0066.10.168556
MA0067.10.724802
MA0068.10.164827
MA0069.10.428576
MA0070.10.419162
MA0071.10.144505
MA0072.10.415392
MA0073.10.633475
MA0074.10.958375
MA0076.16.93185
MA0077.10.408948
MA0078.10.232083
MA0081.10.845052
MA0083.10.447432
MA0084.10.901266
MA0087.10.413345
MA0088.11.98958
MA0089.10
MA0090.10.07671
MA0091.10.109964
MA0092.10.303729
MA0093.12.46622
MA0095.10
MA0098.10
MA0100.10.524766
MA0101.11.02716
MA0103.10.339407
MA0105.10.553815
MA0106.11.07911
MA0107.10.442492
MA0108.20.307261
MA0109.10
MA0111.10.282297
MA0113.10.206168
MA0114.10.224223
MA0115.10.654355
MA0116.10.452238
MA0117.12.07194
MA0119.10.207161
MA0122.10.495633
MA0124.10.616574
MA0125.10.541304
MA0130.10
MA0131.11.27154
MA0132.10
MA0133.10
MA0135.10.466979
MA0136.10.514095
MA0139.11.54878
MA0140.10.142924
MA0141.10.223954
MA0142.10.285297
MA0143.10.594912
MA0144.10.389325
MA0145.10.977277
MA0146.16.06114
MA0147.13.57595
MA0148.10.122067
MA0149.10.137231
MA0062.27.82394
MA0035.20.142505
MA0039.29.41705
MA0138.20.6578
MA0002.20.00996285
MA0137.20.712564
MA0104.24.55226
MA0047.20.187056
MA0112.21.74357
MA0065.20.0824391
MA0150.10.547391
MA0151.10
MA0152.10.146841
MA0153.10.526421
MA0154.10.99413
MA0155.11.96884
MA0156.11.56256
MA0157.10.264816
MA0158.10
MA0159.10.0998181
MA0160.10.130642
MA0161.10
MA0162.11.32955
MA0163.14.36117
MA0164.10.214689
MA0080.20.0409184
MA0018.21.08277
MA0099.20.147056
MA0079.210.3339
MA0102.20.936833
MA0258.10.18561
MA0259.11.55388
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
ATF3#467118.824818563789151.43387867415765e-081.05311430977743e-06
BCL3#60267.402950600801070.0001276408803604870.00169774400203374
BRCA1#67264.325192280690810.002164031464974470.0124887706343852
CCNT2#905184.073272442333129.59358390300145e-097.30280108779569e-07
CHD2#1106114.063723256260193.0800601802331e-050.000628155448473666
CTCF#10664112.105815003708050.00883217986061110.0335341561225275
CTCFL#14069064.231387362637360.002416712809055170.0136203696003947
E2F1#1869213.680541911159498.0805550823931e-107.61665245713045e-08
E2F4#1874104.524307255458733.24655435082012e-050.000646334140002483
E2F6#1876193.404498532223235.14126400499946e-083.28408851020268e-06
EBF1#1879103.180881016631790.0006118206820353750.00507892379072351
EGR1#1958173.02853730756332.93467489205549e-060.000100621966858629
ELF1#1997274.106023031707272.20897816274713e-164.35289566677637e-14
ELK4#2005148.117840829234011.97056937882904e-102.04170927932069e-08
ETS1#2113144.864380461101171.43855917730337e-078.13436285427105e-06
GABPB1#2553194.795928317409331.37311896916134e-101.46333849000246e-08
GTF2F1#2962115.004866773011934.22018104532828e-060.000133723145689636
HEY1#23462253.607242002772969.9905814499289e-131.40620800006621e-10
HMGN3#9324205.841819802393286.40409087271727e-139.2380779924823e-11
IRF1#3659215.727872815172931.32840550682668e-132.05536804040699e-11
JUNB#372644.372947522831590.01245086179013810.0450698583980394
JUND#3727102.498094264953940.003939880248732180.0189411320796051
MAX#4149194.37851980968346.78038983874354e-106.46110524058883e-08
MXI1#4601196.759637890943812.99585529287429e-134.45703890217233e-11
MYC#4609193.543691270020672.60507211470082e-081.80658118583824e-06
NFE2#4778411.02918009308990.0004484814867462330.00417273567877861
NFKB1#4790183.528040772696049.69991054743024e-085.71375610639068e-06
NFYA#480063.948338721392260.003414130659444270.0173986723890749
NFYB#480174.189948313384110.001043787842219270.00738014748179126
NRF1#4899146.105139723855458.03437919924525e-096.20179252912029e-07
PAX5#5079153.572981534559552.28797339117745e-068.15819914650672e-05
POLR2A#5430272.070758420252421.68055752509302e-081.21716884440492e-06
POU2F2#545282.601749730783580.008685490164083290.0330035985900198
RFX5#599383.442260236341460.001535030295322160.00975995549818284
SIN3A#25942234.443012454169585.07578508488072e-137.38314649693394e-11
SIX5#147912106.102398341235362.31496312516378e-068.22915023243637e-05
SMARCB1#659863.911296238819450.003577181418640320.0181208347568209
SMARCC2#6601413.45076777527110.0002119024988859890.00246418940888028
SMC3#912673.761233211233210.001952711601605860.0114695037939438
SP1#6667183.663245171662015.31869636707385e-083.37677404182873e-06
SP2#666876.538382623461166.93660950737152e-050.00110032284377335
SPI1#668892.637103984882310.004639078029458490.0219022951186029
SRF#6722104.927563665059931.54598667385094e-050.000362508536664387
STAT1#677264.437125892256970.001901603717555240.011191344001902
STAT3#677472.629866249288560.01381355326346270.0485912323773249
TAF1#6872263.104257265334914.49895909605899e-125.9177177460114e-10
TAF7#6879124.899886887824531.59055383094714e-066.04717333637744e-05
TBP#6908243.177232017511191.36020450705771e-101.45253986209202e-08
TCF12#693883.038418543481830.003385489801551110.0172864559198297
TCF7L2#693483.077193303753530.003127998936256580.0164386394054094
THAP1#551451314.56424570846678.282200471912e-131.17684997970887e-10
USF1#7391143.180749638603982.47551898685609e-050.000536280289293224
USF2#7392125.568084593601254.04862539498964e-071.94944392635926e-05
YY1#7528244.209574928446162.20226274778884e-133.31893389778238e-11
ZBTB33#1000955.654415183925210.00167901210568490.0104946044231029
ZBTB7A#51341174.463659222638948.83684393123115e-096.77117493275019e-07
ZNF143#7702104.821741625795681.86874630066648e-050.000424282597598492



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:C385&oldid=3067502"