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Coexpression cluster:C3013: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;4.57391,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;1.88666,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;1.77664,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;6.20416,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.9924,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.711948,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;2.48891,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;3.14419,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:04, 22 January 2013


Full id: C3013_Smooth_Fibroblast_hepatic_mesenchymal_basal_spindle_Mesothelial



Phase1 CAGE Peaks

Hg19::chr10:33247124..33247207,-p1@ITGB1
Hg19::chr10:33247223..33247234,-p3@ITGB1
Hg19::chr8:62627160..62627178,-p2@ASPH


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:0031594neuromuscular junction0.0291501513585371
GO:0004597peptide-aspartate beta-dioxygenase activity0.0291501513585371
GO:0042383sarcolemma0.0291501513585371
GO:0008307structural constituent of muscle0.0291501513585371
GO:0001726ruffle0.0291501513585371
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.0291501513585371
GO:0030176integral to endoplasmic reticulum membrane0.0291501513585371
GO:0008305integrin complex0.0291501513585371
GO:0031227intrinsic to endoplasmic reticulum membrane0.0291501513585371
GO:0031252leading edge0.0291501513585371
GO:0006968cellular defense response0.0291501513585371
GO:0051213dioxygenase activity0.0291501513585371
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0291501513585371
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0291501513585371
GO:0048770pigment granule0.0291501513585371
GO:0042470melanosome0.0291501513585371
GO:0007229integrin-mediated signaling pathway0.0291501513585371
GO:0007160cell-matrix adhesion0.0301724825008919
GO:0031589cell-substrate adhesion0.0301724825008919
GO:0046982protein heterodimerization activity0.0301724825008919
GO:0043235receptor complex0.0301724825008919
GO:0018193peptidyl-amino acid modification0.0316759691239406
GO:0031301integral to organelle membrane0.0347967680636087
GO:0031300intrinsic to organelle membrane0.0364586862712288
GO:0003012muscle system process0.0365254835953352
GO:0006936muscle contraction0.0365254835953352
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0377240214046705
GO:0007156homophilic cell adhesion0.0423186472106859
GO:0032501multicellular organismal process0.0427628214148144
GO:0016477cell migration0.0446564411088571
GO:0009055electron carrier activity0.046911570277405



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism9.78e-16656
anatomical system1.37e-14624
anatomical group2.92e-14625
multilaminar epithelium6.23e-1483
surface structure1.94e-1399
dense mesenchyme tissue2.26e-1373
somite2.33e-1371
presomitic mesoderm2.33e-1371
presumptive segmental plate2.33e-1371
dermomyotome2.33e-1371
trunk paraxial mesoderm2.33e-1371
paraxial mesoderm4.01e-1372
presumptive paraxial mesoderm4.01e-1372
organism subdivision1.34e-12264
muscle tissue3.06e-1264
musculature3.06e-1264
musculature of body3.06e-1264
skeletal muscle tissue3.45e-1262
striated muscle tissue3.45e-1262
myotome3.45e-1262
splanchnic layer of lateral plate mesoderm5.33e-1283
mesenchyme9.35e-12160
entire embryonic mesenchyme9.35e-12160
unilaminar epithelium3.14e-11148
trunk mesenchyme3.28e-11122
trunk1.39e-10199
epithelial vesicle2.10e-1078
artery6.52e-1042
arterial blood vessel6.52e-1042
arterial system6.52e-1042
vasculature1.34e-0978
vascular system1.34e-0978
epithelial tube open at both ends2.59e-0959
blood vessel2.59e-0959
blood vasculature2.59e-0959
vascular cord2.59e-0959
integument5.97e-0946
integumental system5.97e-0946
systemic artery8.20e-0933
systemic arterial system8.20e-0933
epithelial tube1.49e-08117
mesoderm2.27e-08315
mesoderm-derived structure2.27e-08315
presumptive mesoderm2.27e-08315
vessel2.93e-0868
skin of body2.98e-0841
circulatory system8.16e-08112
cardiovascular system1.14e-07109
heart3.20e-0724
primitive heart tube3.20e-0724
primary heart field3.20e-0724
anterior lateral plate mesoderm3.20e-0724
heart tube3.20e-0724
heart primordium3.20e-0724
cardiac mesoderm3.20e-0724
cardiogenic plate3.20e-0724
heart rudiment3.20e-0724
multi-tissue structure3.60e-07342
organ component layer3.73e-0766
primary circulatory organ3.98e-0727
developing anatomical structure6.14e-07581
embryo7.59e-07592
embryonic structure8.34e-07564
Disease
Ontology termp-valuen
ovarian cancer1.94e-0814


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)
MA0003.14.57391
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.16.20416
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#90536.336201576962630.003930750035764890.018904199805915
E2F1#186934.907389214879320.008460985347239390.0323375850355096
E2F6#187635.017155731697390.00791769806886330.0320212387164658
EGR1#195834.988179094810140.008056488137383440.0318909780389702
ELF1#199734.258097958807540.01295179875054610.0459795679563644
ELK4#2005210.8237877723120.01091284719516480.0401680005715026
FOSL2#2355211.28680040304110.0100534586973120.0376550413458816
IRF1#365937.63716375356390.002244692747297240.0127555071459262
MYC#460935.22228187160940.007020843755740150.0293053795214318
NR3C1#2908314.9730233311730.0002978331194675480.00307760890116467
REST#597839.650028716128020.001112636247114590.00765145301984596
SIN3A#2594235.408884726815140.006318961977991520.0275264262781838
TFAP2A#7020211.01242291536330.01054990655215560.0389901160833923
TFAP2C#7022310.80922860986020.0007916746575753130.00612774842974195
ZBTB7A#5134137.35190930787590.002516255860282270.0139561999889548



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:C3013&oldid=2571524"