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Coexpression cluster:C1425: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0201011396294926,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.106966425460878,0.163853084473343,0,0.252269924171347,0.359394923119558,0.249834346378391,0.349587664990422,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.11709348206417,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.493914499457327,0.284471418995217,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0463716234329315,0,0,0,0,0,0.0427731395788809,0,0,0,0,0,0,0,0,0.639953219454223,0,0,0,0,0|full_id=C1425_umbilical_skeletal_heart_penis_left_vein_diaphragm|gostat_on_coexpression_clusters=GO:0051393!alpha-actinin binding!0.0119301652014414!7273$GO:0042805!actinin binding!0.0119301652014414!7273$GO:0030239!myofibril assembly!0.0119301652014414!7273$GO:0055001!muscle cell development!0.0119301652014414!7273$GO:0055002!striated muscle cell development!0.0119301652014414!7273$GO:0017022!myosin binding!0.0119301652014414!7273$GO:0048628!myoblast maturation!0.0123024395660017!7273$GO:0048627!myoblast development!0.0123024395660017!7273$GO:0030018!Z disc!0.0138263140820198!7273$GO:0051146!striated muscle cell differentiation!0.0138263140820198!7273$GO:0031674!I band!0.0138263140820198!7273$GO:0031032!actomyosin structure organization and biogenesis!0.0152355730671411!7273$GO:0045445!myoblast differentiation!0.0152355730671411!7273$GO:0015106!bicarbonate transmembrane transporter activity!0.0152355730671411!6508$GO:0000794!condensed nuclear chromosome!0.0152355730671411!7273$GO:0005452!inorganic anion exchanger activity!0.0152355730671411!6508$GO:0015380!anion exchanger activity!0.0152355730671411!6508$GO:0015301!anion:anion antiporter activity!0.0152355730671411!6508$GO:0015108!chloride transmembrane transporter activity!0.0152355730671411!6508$GO:0006941!striated muscle contraction!0.0152355730671411!7273$GO:0048741!skeletal muscle fiber development!0.0152355730671411!7273$GO:0008307!structural constituent of muscle!0.0152355730671411!7273$GO:0048747!muscle fiber development!0.0152355730671411!7273$GO:0046777!protein amino acid autophosphorylation!0.0152355730671411!7273$GO:0048469!cell maturation!0.0152355730671411!7273$GO:0042692!muscle cell differentiation!0.0152355730671411!7273$GO:0016540!protein autoprocessing!0.0152355730671411!7273$GO:0030017!sarcomere!0.0152874174755057!7273$GO:0000793!condensed chromosome!0.0152874174755057!7273$GO:0030016!myofibril!0.0152874174755057!7273$GO:0021700!developmental maturation!0.0152874174755057!7273$GO:0044449!contractile fiber part!0.0167639532257972!7273$GO:0043292!contractile 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|full_id=C1425_umbilical_skeletal_heart_penis_left_vein_diaphragm
|id=C1425
}}

Latest revision as of 11:44, 17 September 2013


Full id: C1425_umbilical_skeletal_heart_penis_left_vein_diaphragm



Phase1 CAGE Peaks

Hg19::chr16:7382818..7382819,+p40@RBFOX1
Hg19::chr2:106115231..106115234,+p@chr2:106115231..106115234
+
Hg19::chr2:179629521..179629528,-p138@TTN
Hg19::chr2:220495902..220495903,+p25@SLC4A3
Hg19::chr4:100578977..100578989,-p@chr4:100578977..100578989
-
Hg19::chr4:23890694..23890699,-p@chr4:23890694..23890699
-


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:0051393alpha-actinin binding0.0119301652014414
GO:0042805actinin binding0.0119301652014414
GO:0030239myofibril assembly0.0119301652014414
GO:0055001muscle cell development0.0119301652014414
GO:0055002striated muscle cell development0.0119301652014414
GO:0017022myosin binding0.0119301652014414
GO:0048628myoblast maturation0.0123024395660017
GO:0048627myoblast development0.0123024395660017
GO:0030018Z disc0.0138263140820198
GO:0051146striated muscle cell differentiation0.0138263140820198
GO:0031674I band0.0138263140820198
GO:0031032actomyosin structure organization and biogenesis0.0152355730671411
GO:0045445myoblast differentiation0.0152355730671411
GO:0015106bicarbonate transmembrane transporter activity0.0152355730671411
GO:0000794condensed nuclear chromosome0.0152355730671411
GO:0005452inorganic anion exchanger activity0.0152355730671411
GO:0015380anion exchanger activity0.0152355730671411
GO:0015301anion:anion antiporter activity0.0152355730671411
GO:0015108chloride transmembrane transporter activity0.0152355730671411
GO:0006941striated muscle contraction0.0152355730671411
GO:0048741skeletal muscle fiber development0.0152355730671411
GO:0008307structural constituent of muscle0.0152355730671411
GO:0048747muscle fiber development0.0152355730671411
GO:0046777protein amino acid autophosphorylation0.0152355730671411
GO:0048469cell maturation0.0152355730671411
GO:0042692muscle cell differentiation0.0152355730671411
GO:0016540protein autoprocessing0.0152355730671411
GO:0030017sarcomere0.0152874174755057
GO:0000793condensed chromosome0.0152874174755057
GO:0030016myofibril0.0152874174755057
GO:0021700developmental maturation0.0152874174755057
GO:0044449contractile fiber part0.0167639532257972
GO:0043292contractile fiber0.0173386632132831
GO:0007519skeletal muscle development0.0176167693313917
GO:0015103inorganic anion transmembrane transporter activity0.0181340618399547
GO:0014706striated muscle development0.0218462131870707
GO:0015297antiporter activity0.0219794318898589
GO:0016485protein processing0.0226827744463691
GO:0000228nuclear chromosome0.0226827744463691
GO:0005516calmodulin binding0.031478625965811
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0327321340518741
GO:0035023regulation of Rho protein signal transduction0.0327321340518741
GO:0003012muscle system process0.0327321340518741
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0327321340518741
GO:0006936muscle contraction0.0327321340518741
GO:0007517muscle development0.0333755668419712
GO:0007266Rho protein signal transduction0.0356956654106276
GO:0008509anion transmembrane transporter activity0.0388441760135324
GO:0007067mitosis0.0431821166596885
GO:0000087M phase of mitotic cell cycle0.0431821166596885
GO:0030036actin cytoskeleton organization and biogenesis0.0431821166596885
GO:0030029actin filament-based process0.0445721666664363



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
primary circulatory organ2.86e-2727
valve3.63e-213
cardiac mesenchyme3.63e-213
cardial valve3.63e-213
tunica intima3.63e-213
heart layer3.63e-213
endocardium3.63e-213
endocardial cushion3.63e-213
presumptive endocardium3.63e-213
hindlimb bud5.53e-171
soleus muscle5.53e-171
appendage5.53e-171
lower limb segment5.53e-171
multi-limb segment region5.53e-171
hindlimb muscle5.53e-171
hindlimb zeugopod muscle5.53e-171
paired limb/fin5.53e-171
limb5.53e-171
pelvic appendage5.53e-171
limb segment5.53e-171
paired limb/fin segment5.53e-171
limb muscle5.53e-171
pelvic complex muscle5.53e-171
zeugopod5.53e-171
muscle of leg5.53e-171
paired limb/fin bud5.53e-171
limb bud5.53e-171
pelvic appendage bud5.53e-171
limb/fin field5.53e-171
subdivision of organism along appendicular axis5.53e-171
appendage girdle complex5.53e-171
leg5.53e-171
hindlimb5.53e-171
triceps surae5.53e-171
hindlimb zeugopod5.53e-171
posterior region of body5.53e-171
pelvic complex5.53e-171
limb field5.53e-171
hindlimb/pelvic fin field5.53e-171
pulmonary valve1.41e-161
semi-lunar valve1.41e-161
left cardiac atrium1.65e-161
mitral valve1.93e-161
compound organ9.77e-1468
adult organism1.84e-12114
heart1.77e-1024
primitive heart tube1.77e-1024
primary heart field1.77e-1024
anterior lateral plate mesoderm1.77e-1024
heart tube1.77e-1024
heart primordium1.77e-1024
cardiac mesoderm1.77e-1024
cardiogenic plate1.77e-1024
heart rudiment1.77e-1024
blood vessel layer1.24e-097
muscle structure3.71e-092
muscle organ3.71e-092
cardiac atrium6.42e-092
future cardiac atrium6.42e-092
atrioventricular valve6.94e-092
throat7.49e-092
neural crest-derived structure5.26e-0710
neural crest5.26e-0710
neural fold5.26e-0710
Disease
Ontology termp-valuen
heart disease8.57e-322
vascular disease1.04e-161
ischemia1.04e-161
extrinsic cardiomyopathy1.04e-161
myocardial ischemia1.04e-161
myocardial infarction1.04e-161
cardiovascular system disease1.93e-164


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.09642
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.11.53717
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.200862
MA0138.21.80506
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.166826
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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

No analysis results for this cluster

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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