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Coexpression cluster:C389: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C389_heart_left_umbilical_skin_skeletal_trachea_throat
 

Latest revision as of 11:21, 17 September 2013


Full id: C389_heart_left_umbilical_skin_skeletal_trachea_throat



Phase1 CAGE Peaks

Hg19::chr10:25242626..25242636,-p@chr10:25242626..25242636
-
Hg19::chr12:114886577..114886589,-p@chr12:114886577..114886589
-
Hg19::chr12:4735761..4735787,-p@chr12:4735761..4735787
-
Hg19::chr13:93329902..93329916,-p@chr13:93329902..93329916
-
Hg19::chr14:23853394..23853399,-p@chr14:23853394..23853399
-
Hg19::chr14:23854188..23854193,-p@chr14:23854188..23854193
-
Hg19::chr14:23854202..23854211,-p@chr14:23854202..23854211
-
Hg19::chr14:23862577..23862585,-p5@MYH6
Hg19::chr14:23862929..23862940,-p@chr14:23862929..23862940
-
Hg19::chr14:23863036..23863066,-p@chr14:23863036..23863066
-
Hg19::chr14:23863088..23863103,-p@chr14:23863088..23863103
-
Hg19::chr14:23863108..23863123,-p@chr14:23863108..23863123
-
Hg19::chr14:23863373..23863402,-p@chr14:23863373..23863402
-
Hg19::chr14:23863442..23863452,-p@chr14:23863442..23863452
-
Hg19::chr14:23867985..23867992,-p@chr14:23867985..23867992
-
Hg19::chr14:23872542..23872556,-p@chr14:23872542..23872556
-
Hg19::chr14:23876809..23876833,-p8@MYH6
Hg19::chr14:23877474..23877491,-p1@MYH6
Hg19::chr19:56057552..56057564,-p@chr19:56057552..56057564
-
Hg19::chr2:159976509..159976519,+p@chr2:159976509..159976519
+
Hg19::chr3:178103144..178103153,-p1@ENST00000417383
Hg19::chr4:174926997..174927004,+p@chr4:174926997..174927004
+
Hg19::chr5:117897774..117897788,-p1@ENST00000506769
p1@ENST00000515704
Hg19::chr5:148803658..148803668,+p@chr5:148803658..148803668
+
Hg19::chr7:25815812..25815822,-p@chr7:25815812..25815822
-
Hg19::chr7:44178491..44178498,-p@chr7:44178491..44178498
-
Hg19::chr8:111668033..111668039,+p@chr8:111668033..111668039
+


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:0055009atrial cardiac muscle morphogenesis0.00230254981226369
GO:0030898actin-dependent ATPase activity0.00230254981226369
GO:0030049muscle filament sliding0.00230254981226369
GO:0033275actin-myosin filament sliding0.00230254981226369
GO:0002027regulation of heart rate0.00230254981226369
GO:0055010ventricular cardiac muscle morphogenesis0.00230254981226369
GO:0007512adult heart development0.00230254981226369
GO:0048644muscle morphogenesis0.00230254981226369
GO:0055008cardiac muscle morphogensis0.00230254981226369
GO:0000146microfilament motor activity0.00318814589390358
GO:0030048actin filament-based movement0.00318814589390358
GO:0032982myosin filament0.00318814589390358
GO:0005863striated muscle thick filament0.00318814589390358
GO:0005859muscle myosin complex0.0044899721339142
GO:0016460myosin II complex0.0044899721339142
GO:0006941striated muscle contraction0.00592084237439235
GO:0008016regulation of heart contraction0.00592084237439235
GO:0008307structural constituent of muscle0.00592084237439235
GO:0060047heart contraction0.00592084237439235
GO:0003015heart process0.00592084237439235
GO:0030017sarcomere0.00592084237439235
GO:0030016myofibril0.00624043329801013
GO:0044449contractile fiber part0.00675748314468692
GO:0043292contractile fiber0.00690764943679108
GO:0007507heart development0.00973978570587542
GO:0016459myosin complex0.0106603628327401
GO:0005516calmodulin binding0.0135274801470492
GO:0008015blood circulation0.0137874454484338
GO:0003013circulatory system process0.0137874454484338
GO:0003012muscle system process0.0137874454484338
GO:0006936muscle contraction0.0137874454484338
GO:0007517muscle development0.013923230896032
GO:0030705cytoskeleton-dependent intracellular transport0.0153852192001256
GO:0030029actin filament-based process0.019808700590798
GO:0051239regulation of multicellular organismal process0.0205009167213335
GO:0015629actin cytoskeleton0.0212985857634392
GO:0009887organ morphogenesis0.0253436057039024
GO:0003779actin binding0.0298574057892878
GO:0042623ATPase activity, coupled0.0350696048329393
GO:0008092cytoskeletal protein binding0.0390498057223596
GO:0016887ATPase activity0.0397400441683682
GO:0007010cytoskeleton organization and biogenesis0.0423093528003454



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
valve3.54e-743
cardiac mesenchyme3.54e-743
cardial valve3.54e-743
tunica intima3.54e-743
heart layer3.54e-743
endocardium3.54e-743
endocardial cushion3.54e-743
presumptive endocardium3.54e-743
primary circulatory organ3.24e-5827
atrioventricular valve3.11e-502
cardiac atrium4.00e-502
future cardiac atrium4.00e-502
cardiac chamber7.70e-343
blood vessel layer2.31e-327
mitral valve2.16e-261
left cardiac atrium2.78e-261
heart4.95e-2624
primitive heart tube4.95e-2624
primary heart field4.95e-2624
anterior lateral plate mesoderm4.95e-2624
heart tube4.95e-2624
heart primordium4.95e-2624
cardiac mesoderm4.95e-2624
cardiogenic plate4.95e-2624
heart rudiment4.95e-2624
pulmonary valve7.62e-261
semi-lunar valve7.62e-261
tricuspid valve9.79e-261
right atrium valve9.79e-261
outflow tract of atrium9.79e-261
outflow part of right atrium9.79e-261
right cardiac atrium9.79e-261
compound organ2.94e-2368
neural crest-derived structure6.42e-2310
neural crest6.42e-2310
neural fold6.42e-2310
circulatory system3.77e-14112
adult organism1.15e-10114
outflow tract1.67e-093
splanchnic layer of lateral plate mesoderm1.03e-0783
Disease
Ontology termp-valuen
heart disease3.11e-502
vascular disease5.93e-261
ischemia5.93e-261
extrinsic cardiomyopathy5.93e-261
myocardial ischemia5.93e-261
myocardial infarction5.93e-261
cardiovascular system disease9.82e-264


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)
MA0003.19.29738e-07
MA0004.10.744999
MA0006.10.043712
MA0007.10.699342
MA0009.10.45361
MA0014.10.00175617
MA0017.11.71139
MA0019.10.206961
MA0024.10.366071
MA0025.10.570597
MA0027.12.00534
MA0028.10.185296
MA0029.10.381857
MA0030.10.372472
MA0031.10.320773
MA0038.10.176878
MA0040.10.38667
MA0041.10.125771
MA0042.10.108251
MA0043.10.453881
MA0046.10.444311
MA0048.10.194996
MA0050.10.351951
MA0051.10.517477
MA0052.10.389861
MA0055.10.47967
MA0056.10
MA0057.10.18052
MA0058.11.85666
MA0059.11.3324
MA0060.10.0133608
MA0061.10.0465062
MA0063.10
MA0066.10.177154
MA0067.10.739032
MA0068.10.0831041
MA0069.10.441028
MA0070.10.431528
MA0071.10.905737
MA0072.10.427724
MA0073.10.0824041
MA0074.10.516295
MA0076.10.0757217
MA0077.10.421218
MA0078.10.242013
MA0081.10.240854
MA0083.12.02795
MA0084.10.916043
MA0087.10.425657
MA0088.10.0109451
MA0089.10
MA0090.10.280795
MA0091.10.751442
MA0092.10.0969694
MA0093.11.06288
MA0095.10
MA0098.10
MA0100.10.546121
MA0101.10.0459133
MA0103.10.361926
MA0105.10.0288952
MA0106.10.204305
MA0107.10.023874
MA0108.20.853131
MA0109.10
MA0111.10.0888583
MA0113.11.15924
MA0114.11.08668
MA0115.11.60402
MA0116.10.105451
MA0117.10.486035
MA0119.10.221145
MA0122.10.50863
MA0124.10.630319
MA0125.10.554615
MA0130.10
MA0131.10.255226
MA0132.10
MA0133.10
MA0135.10.479757
MA0136.10.181467
MA0139.10.113289
MA0140.10.459966
MA0141.10.878913
MA0142.11.45957
MA0143.11.15972
MA0144.10.0863774
MA0145.10.601271
MA0146.10.00299613
MA0147.10.263899
MA0148.10.405671
MA0149.10.874165
MA0062.20.0434959
MA0035.20.458892
MA0039.20.126888
MA0138.20.242899
MA0002.20.151075
MA0137.20.192569
MA0104.20.167263
MA0047.20.570534
MA0112.20.0796372
MA0065.20.62147
MA0150.10.0796342
MA0151.10
MA0152.10.47
MA0153.10.539635
MA0154.10.00749586
MA0155.10.0703467
MA0156.10.432724
MA0157.10.275302
MA0158.10
MA0159.10.793879
MA0160.10.428183
MA0161.10
MA0162.10.0060798
MA0163.10.0141236
MA0164.10.224291
MA0080.20.687581
MA0018.20.205249
MA0099.20.155103
MA0079.22.51259e-05
MA0102.20.951693
MA0258.10.017374
MA0259.10.279278
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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