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Coexpression cluster:C1147: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.0712,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;3.71689,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;2.50576,MA0027.1;2.59001,MA0028.1;2.53091,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;1.8235,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.158296,MA0056.1;0,MA0057.1;0.369442,MA0058.1;0.406232,MA0059.1;1.04442,MA0060.1;1.19421,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.946606,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;3.16596,MA0074.1;1.46532,MA0076.1;3.86616,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.252594,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.547495,MA0140.1;0.564957,MA0141.1;1.04059,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.708913,MA0145.1;0.276317,MA0146.1;1.97205,MA0147.1;0.768766,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;2.39331,MA0035.2;0.564239,MA0039.2;3.10611,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;1.19136,MA0047.2;0.636643,MA0112.2;0.556641,MA0065.2;0.591589,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.685508,MA0155.1;0.910701,MA0156.1;0.959643,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.770207,MA0160.1;0.543522,MA0161.1;0,MA0162.1;1.13878,MA0163.1;1.72058,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;1.56673,MA0099.2;0.572,MA0079.2;3.65327,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;1.43531,MA0442.1;0
}}
}}

Revision as of 19:44, 22 January 2013


Full id: C1147_Mesenchymal_Renal_Alveolar_Fibroblast_Placental_Pericytes_Hepatic



Phase1 CAGE Peaks

Hg19::chr11:64851666..64851728,+p1@ZFPL1
Hg19::chr11:66056596..66056622,-p1@YIF1A
Hg19::chr19:11039271..11039355,-p1@YIPF2
Hg19::chr19:38806561..38806607,-p1@YIF1B
Hg19::chr1:44444865..44444930,+p1@B4GALT2
Hg19::chr5:180229833..180229860,-p3@MGAT1
Hg19::chr6:43484621..43484706,-p1@YIPF3


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

p.valueFDRnGenesnPathwayName
6.02832773164619e-050.0381593145413204249N-Glycan biosynthesis (KEGG):00510



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:0016021integral to membrane0.000580518378430204
GO:0031224intrinsic to membrane0.000580518378430204
GO:0044425membrane part0.00101525068808855
GO:0030133transport vesicle0.00171329991318636
GO:0016020membrane0.0031001539715636
GO:0005794Golgi apparatus0.00453665188376353
GO:0008194UDP-glycosyltransferase activity0.00470395734307677
GO:0003831beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity0.00666117273112001
GO:0004461lactose synthase activity0.00666117273112001
GO:0044444cytoplasmic part0.00722897183027535
GO:0003945N-acetyllactosamine synthase activity0.00726609217133451
GO:0003827alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity0.00832499538422828
GO:0016758transferase activity, transferring hexosyl groups0.0103938426317109
GO:0043231intracellular membrane-bound organelle0.0108150443212596
GO:0043227membrane-bound organelle0.0108150443212596
GO:0016023cytoplasmic membrane-bound vesicle0.0123942685714032
GO:0031988membrane-bound vesicle0.0123942685714032
GO:0000139Golgi membrane0.0125714635726644
GO:0044431Golgi apparatus part0.0147521770957566
GO:0031410cytoplasmic vesicle0.0147521770957566
GO:0031982vesicle0.0147521770957566
GO:0016757transferase activity, transferring glycosyl groups0.0147521770957566
GO:0035250UDP-galactosyltransferase activity0.0147521770957566
GO:0006023aminoglycan biosynthetic process0.0174578072166668
GO:0043229intracellular organelle0.0192729000207756
GO:0043226organelle0.0192729000207756
GO:0005737cytoplasm0.0260771053646539
GO:0008378galactosyltransferase activity0.0284547695479466
GO:0005793ER-Golgi intermediate compartment0.0295262676453299
GO:0008375acetylglucosaminyltransferase activity0.0298643231755696
GO:0006022aminoglycan metabolic process0.0319533690155563
GO:0005975carbohydrate metabolic process0.0319533690155563
GO:0006487protein amino acid N-linked glycosylation0.0319533690155563
GO:0044424intracellular part0.0413708282874496
GO:0012505endomembrane system0.0481188913306716



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 vesicle7.28e-2378
mesenchyme7.45e-22160
entire embryonic mesenchyme7.45e-22160
organism subdivision1.82e-21264
unilaminar epithelium9.28e-21148
multilaminar epithelium2.99e-2083
dense mesenchyme tissue7.26e-2073
somite8.03e-2071
presomitic mesoderm8.03e-2071
presumptive segmental plate8.03e-2071
dermomyotome8.03e-2071
trunk paraxial mesoderm8.03e-2071
trunk8.51e-20199
trunk mesenchyme1.36e-19122
paraxial mesoderm2.60e-1972
presumptive paraxial mesoderm2.60e-1972
vasculature3.81e-1978
vascular system3.81e-1978
epithelial tube2.27e-18117
skeletal muscle tissue6.06e-1862
striated muscle tissue6.06e-1862
myotome6.06e-1862
muscle tissue6.75e-1764
musculature6.75e-1764
musculature of body6.75e-1764
splanchnic layer of lateral plate mesoderm1.23e-1683
vessel3.43e-1668
cell layer7.58e-16309
epithelium2.33e-15306
artery3.43e-1542
arterial blood vessel3.43e-1542
arterial system3.43e-1542
epithelial tube open at both ends6.83e-1559
blood vessel6.83e-1559
blood vasculature6.83e-1559
vascular cord6.83e-1559
multi-tissue structure4.66e-13342
cardiovascular system1.58e-12109
multi-cellular organism1.67e-12656
circulatory system2.01e-12112
systemic artery1.78e-1133
systemic arterial system1.78e-1133
anatomical cluster1.40e-10373
anatomical group3.15e-10625
anatomical system4.30e-10624
surface structure9.97e-0999
anatomical conduit2.61e-08240
subdivision of trunk5.30e-08112
urinary system structure7.92e-0847
renal system1.41e-0748


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)
MA0003.12.0712
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.13.71689
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.12.50576
MA0027.12.59001
MA0028.12.53091
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.8235
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.11.04442
MA0060.11.19421
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.946606
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.13.16596
MA0074.11.46532
MA0076.13.86616
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.276317
MA0146.11.97205
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.22.39331
MA0035.20.564239
MA0039.23.10611
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.19136
MA0047.20.636643
MA0112.20.556641
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.910701
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.11.72058
MA0164.10.678332
MA0080.20.344472
MA0018.21.56673
MA0099.20.572
MA0079.23.65327
MA0102.21.51913
MA0258.10.245543
MA0259.11.43531
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
BRCA1#67238.650384561381610.003659293331202230.0184740627552294
CCNT2#90554.525858269259020.00155157330626470.00985553853138175
CEBPB#105144.554941500471320.006321080333068460.0275276169170768
E2F1#186964.206333612753710.0004135232017007640.0039365554336365
E2F6#187664.300419198597760.000363797504290860.00363202825261764
EGR1#195853.562985067721530.004722351211058930.0222582199716483
ELF1#199753.041498542005380.009719562269370750.0365617837433659
ELK4#200549.277532376267440.0004328178589665770.00404140048034066
ETS1#211356.949114944430240.0002014062633330390.00239329488408684
GABPB1#255344.038676477818380.00980113494696150.0368447459767372
GTF2F1#296247.279806215290090.001094056879164720.00764756083281467
HDAC2#306635.749551529982680.01153041704040530.0421706550386221
HEY1#2346274.040111043105715.68979821988558e-050.000949715256970801
IRF1#365955.455116966831360.00064157947210550.0052586657108167
MAX#414943.68717457657550.01360570643953340.0480137311991359
MXI1#460145.692326645005310.002766905405391560.015160423568212
MYC#460964.476241604236630.0002883611950910820.00306338672099659
PAX5#507943.811180303530190.01208261681555190.043826500107645
POLR2A#543072.147453176558070.004747636447610280.0223280228284761
RFX5#599358.605650590853647.16524263203101e-050.00112717393469903
SIN3A#2594264.636186908698690.0002351678146357830.00256508526295002
SIX5#14791249.763837345976570.0003555371351068720.00355840372337581
SREBF1#6720213.43024269728240.008849476021677450.0335912781212463
SRF#672247.884101864095890.0008074788728092760.00616554218433455
TAF1#687262.865468244924540.003728330207471460.0185845302853242
TAF7#687946.533182517099380.00164849410947510.0103112580882476
YY1#752853.507979107038470.005072570672808980.023613737842545
ZBTB7A#5134144.201091033071940.00849410661287350.0324250155540003



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:C1147&oldid=2569658"