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Coexpression cluster:C188: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:52, 17 September 2013


Full id: C188_left_heart_tongue_skeletal_Skeletal_diaphragm_throat



Phase1 CAGE Peaks

Hg19::chr10:127569398..127569410,-p5@DHX32
Hg19::chr10:77945410..77945435,+p@chr10:77945410..77945435
+
Hg19::chr10:92725775..92725780,+p@chr10:92725775..92725780
+
Hg19::chr12:114886372..114886399,-p@chr12:114886372..114886399
-
Hg19::chr12:114886422..114886429,-p@chr12:114886422..114886429
-
Hg19::chr12:3309741..3309748,+p@chr12:3309741..3309748
+
Hg19::chr12:56080980..56080982,+p@chr12:56080980..56080982
+
Hg19::chr12:70004523..70004545,-p3@LRRC10
Hg19::chr12:70004575..70004590,-p4@LRRC10
Hg19::chr12:94730118..94730123,-p13@CCDC41
Hg19::chr13:111935498..111935509,+p35@ARHGEF7
Hg19::chr13:24334287..24334315,-p@chr13:24334287..24334315
-
Hg19::chr14:104408818..104408833,-p2@ENST00000557640
Hg19::chr14:23852481..23852521,-p@chr14:23852481..23852521
-
Hg19::chr14:23856796..23856821,+p@chr14:23856796..23856821
+
Hg19::chr14:23862653..23862669,+p@chr14:23862653..23862669
+
Hg19::chr14:23862685..23862696,+p@chr14:23862685..23862696
+
Hg19::chr14:23862698..23862705,+p@chr14:23862698..23862705
+
Hg19::chr14:23862866..23862886,+p@chr14:23862866..23862886
+
Hg19::chr14:23862999..23863032,+p@chr14:23862999..23863032
+
Hg19::chr14:23863078..23863082,+p@chr14:23863078..23863082
+
Hg19::chr14:23863529..23863540,-p@chr14:23863529..23863540
-
Hg19::chr14:23866230..23866266,-p@chr14:23866230..23866266
-
Hg19::chr15:26640200..26640207,+p3@ENST00000451579
Hg19::chr15:26640223..26640233,+p2@ENST00000451579
Hg19::chr15:26640236..26640246,+p1@ENST00000451579
Hg19::chr15:26640258..26640266,+p4@ENST00000451579
Hg19::chr15:26640282..26640290,+p5@ENST00000451579
Hg19::chr15:35082732..35082764,-p@chr15:35082732..35082764
-
Hg19::chr15:44171970..44171983,-p@chr15:44171970..44171983
-
Hg19::chr15:65042595..65042606,-p@chr15:65042595..65042606
-
Hg19::chr15:65042618..65042632,-p@chr15:65042618..65042632
-
Hg19::chr15:77964112..77964131,-p@chr15:77964112..77964131
-
Hg19::chr15:77964143..77964150,-p@chr15:77964143..77964150
-
Hg19::chr15:83474864..83474869,-p4@FSD2
Hg19::chr17:45286706..45286723,+p1@MYL4
Hg19::chr17:4806374..4806394,-p1@CHRNE
Hg19::chr17:65440428..65440449,-p@chr17:65440428..65440449
-
Hg19::chr18:21906552..21906584,+p@chr18:21906552..21906584
+
Hg19::chr18:28807557..28807562,-p@chr18:28807557..28807562
-
Hg19::chr19:3933460..3933476,+p2@ITGB1BP3
Hg19::chr19:3933579..3933594,+p1@ITGB1BP3
Hg19::chr1:109849612..109849651,-p1@MYBPHL
Hg19::chr1:109849679..109849688,-p3@MYBPHL
Hg19::chr1:11905799..11905806,-p@chr1:11905799..11905806
-
Hg19::chr1:11905830..11905839,-p@chr1:11905830..11905839
-
Hg19::chr1:11905915..11905921,-p@chr1:11905915..11905921
-
Hg19::chr1:11906020..11906041,+p@chr1:11906020..11906041
+
Hg19::chr1:11906044..11906050,-p@chr1:11906044..11906050
-
Hg19::chr1:11907265..11907271,-p9@NPPA
Hg19::chr1:11907318..11907327,-p7@NPPA
Hg19::chr1:11907395..11907410,-p4@NPPA
Hg19::chr1:11907408..11907415,+p@chr1:11907408..11907415
+
Hg19::chr1:11907415..11907418,-p15@NPPA
Hg19::chr1:11907440..11907450,+p@chr1:11907440..11907450
+
Hg19::chr1:11907441..11907453,-p3@NPPA
Hg19::chr1:11907474..11907481,-p10@NPPA
Hg19::chr1:11907829..11907847,-p1@NPPA
Hg19::chr1:11907940..11907947,-p2@NPPA
Hg19::chr1:201342333..201342350,+p@chr1:201342333..201342350
+
Hg19::chr1:233842857..233842870,-p@chr1:233842857..233842870
-
Hg19::chr1:43676416..43676417,-p@chr1:43676416..43676417
-
Hg19::chr2:149639329..149639360,-p@chr2:149639329..149639360
-
Hg19::chr2:179655525..179655536,-p@chr2:179655525..179655536
-
Hg19::chr2:27938986..27938991,+p@chr2:27938986..27938991
+
Hg19::chr3:42744130..42744141,-p4@HHATL
Hg19::chr4:111536685..111536696,-p2@ENST00000513690
Hg19::chr4:13842523..13842533,-p@chr4:13842523..13842533
-
Hg19::chr4:47833348..47833366,+p@chr4:47833348..47833366
+
Hg19::chr4:65180453..65180460,-p1@AX771276
Hg19::chr4:65366184..65366190,-p@chr4:65366184..65366190
-
Hg19::chr4:8321842..8321846,+p5@ENST00000509453
Hg19::chr5:102201562..102201573,+p7@PAM
Hg19::chr5:102201574..102201598,+p4@PAM
Hg19::chr5:102201610..102201628,+p3@PAM
Hg19::chr5:172671810..172671816,-p@chr5:172671810..172671816
-
Hg19::chr5:65736120..65736128,-p@chr5:65736120..65736128
-
Hg19::chr5:65736176..65736194,-p@chr5:65736176..65736194
-
Hg19::chr6:118869482..118869497,+p2@PLN
Hg19::chr6:118869507..118869518,+p3@PLN
Hg19::chr6:118880031..118880048,+p5@PLN
Hg19::chr6:118880085..118880101,+p4@PLN
Hg19::chr7:44178513..44178525,+p@chr7:44178513..44178525
+
Hg19::chr7:44179972..44179982,-p2@MYL7
Hg19::chr7:44180643..44180652,-p3@MYL7
Hg19::chr7:44180921..44180937,-p1@MYL7
Hg19::chr8:19540485..19540506,-p20@CSGALNACT1
Hg19::chr8:52567465..52567476,-p@chr8:52567465..52567476
-
Hg19::chr9:134165281..134165287,+p3@PPAPDC3


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:0003012muscle system process0.00281616180046562
GO:0006936muscle contraction0.00281616180046562
GO:0004598peptidylamidoglycolate lyase activity0.0276698457553279
GO:0016459myosin complex0.0331984391158079
GO:0042030ATPase inhibitor activity0.0331984391158079
GO:0004504peptidylglycine monooxygenase activity0.0347557543960679
GO:0045822negative regulation of heart contraction0.0347557543960679
GO:0008015blood circulation0.0347557543960679
GO:0003013circulatory system process0.0347557543960679
GO:0003008system process0.0347557543960679
GO:0007517muscle development0.0347557543960679
GO:0002026regulation of the force of heart contraction0.0432322685227638
GO:0048738cardiac muscle development0.0432322685227638
GO:0055082cellular chemical homeostasis0.0432322685227638
GO:0006873cellular ion homeostasis0.0432322685227638
GO:0016842amidine-lyase activity0.0432322685227638
GO:0050801ion homeostasis0.0432322685227638
GO:0016715oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen0.0432322685227638
GO:0005246calcium channel regulator activity0.0432322685227638
GO:0065008regulation of biological quality0.0432322685227638
GO:0051924regulation of calcium ion transport0.0432322685227638
GO:0005790smooth endoplasmic reticulum0.0432322685227638
GO:0007271synaptic transmission, cholinergic0.0432322685227638
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0443017627326371
GO:0015629actin cytoskeleton0.0443017627326371
GO:0048878chemical homeostasis0.0443017627326371
GO:0000146microfilament motor activity0.0443687273673285
GO:0016840carbon-nitrogen lyase activity0.0443687273673285
GO:0030048actin filament-based movement0.0456872947973257
GO:0043269regulation of ion transport0.046917065715841



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
valve1.54e-663
cardiac mesenchyme1.54e-663
cardial valve1.54e-663
tunica intima1.54e-663
heart layer1.54e-663
endocardium1.54e-663
endocardial cushion1.54e-663
presumptive endocardium1.54e-663
cardiac chamber1.92e-663
primary circulatory organ2.67e-6527
cardiac atrium3.19e-452
future cardiac atrium3.19e-452
atrioventricular valve4.00e-452
heart4.19e-3324
primitive heart tube4.19e-3324
primary heart field4.19e-3324
anterior lateral plate mesoderm4.19e-3324
heart tube4.19e-3324
heart primordium4.19e-3324
cardiac mesoderm4.19e-3324
cardiogenic plate4.19e-3324
heart rudiment4.19e-3324
blood vessel layer4.66e-297
compound organ5.95e-2668
left cardiac atrium1.07e-231
mitral valve1.34e-231
tricuspid valve2.10e-231
right atrium valve2.10e-231
outflow tract of atrium2.10e-231
outflow part of right atrium2.10e-231
right cardiac atrium2.10e-231
pulmonary valve2.62e-231
semi-lunar valve2.62e-231
heart left ventricle4.10e-231
cardiac ventricle4.10e-231
future cardiac ventricle4.10e-231
neural crest-derived structure1.37e-2010
neural crest1.37e-2010
neural fold1.37e-2010
circulatory system1.04e-15112
adult organism3.69e-12114
splanchnic layer of lateral plate mesoderm1.28e-0983
outflow tract1.04e-083
cardiovascular system2.64e-07109
epithelial tube8.49e-07117
Disease
Ontology termp-valuen
heart disease4.65e-442
vascular disease6.40e-231
ischemia6.40e-231
extrinsic cardiomyopathy6.40e-231
myocardial ischemia6.40e-231
myocardial infarction6.40e-231
cardiovascular system disease1.25e-224


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)
MA0003.10.000154811
MA0004.10.281587
MA0006.10.185115
MA0007.10.0170628
MA0009.10.378498
MA0014.18.84589e-05
MA0017.11.33274
MA0019.10.978314
MA0024.10.0738464
MA0025.11.67765
MA0027.11.49225
MA0028.10.0292882
MA0029.12.01938
MA0030.10.0768283
MA0031.10.0542754
MA0038.10.529635
MA0040.10.284231
MA0041.10.176398
MA0042.10.135252
MA0043.10.760933
MA0046.10.113665
MA0048.10.691055
MA0050.10.0591216
MA0051.10.0558947
MA0052.11.50509
MA0055.10.112697
MA0056.10
MA0057.10.1751
MA0058.10.00568307
MA0059.10.0212252
MA0060.10.00460793
MA0061.10.206336
MA0063.10
MA0066.11.13247
MA0067.10.314198
MA0068.10.0343419
MA0069.10.728659
MA0070.10.346551
MA0071.11.66315
MA0072.10.341128
MA0073.10.0761687
MA0074.10.30352
MA0076.10.142454
MA0077.10.101175
MA0078.10.113796
MA0081.10.214781
MA0083.10.776514
MA0084.10.459529
MA0087.10.10353
MA0088.10.0909904
MA0089.10
MA0090.10.880776
MA0091.10.960477
MA0092.10.359405
MA0093.10.110427
MA0095.10
MA0098.10
MA0100.10.338817
MA0101.10.0250883
MA0103.10.554262
MA0105.10.0560877
MA0106.10.0175149
MA0107.10.00160042
MA0108.22.17012
MA0109.10
MA0111.10.702925
MA0113.10.223823
MA0114.11.12755
MA0115.14.69528
MA0116.10.44433
MA0117.10.426761
MA0119.10.451674
MA0122.10.461265
MA0124.10.23275
MA0125.10.180721
MA0130.10
MA0131.10.126975
MA0132.10
MA0133.10
MA0135.10.417297
MA0136.10.0612768
MA0139.10.00123679
MA0140.11.64548
MA0141.15.96201
MA0142.10.171117
MA0143.10.428026
MA0144.10.153505
MA0145.10.00945969
MA0146.10.00189502
MA0147.10.0812765
MA0148.10.0845697
MA0149.10.00689491
MA0062.20.011251
MA0035.24.6404
MA0039.21.99995e-05
MA0138.22.61965
MA0002.20.182809
MA0137.20.139941
MA0104.20.0894453
MA0047.20.368659
MA0112.20.505062
MA0065.20.620247
MA0150.10.0764368
MA0151.10
MA0152.10.437585
MA0153.10.17096
MA0154.14.03716
MA0155.11.88759
MA0156.10.0754673
MA0157.10.0374941
MA0158.10
MA0159.13.50017
MA0160.12.32788
MA0161.10
MA0162.19.33109e-07
MA0163.10.0236349
MA0164.10.736316
MA0080.20.4441
MA0018.20.0177289
MA0099.20.252061
MA0079.20.000697949
MA0102.20.490261
MA0258.10.558477
MA0259.10.022149
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

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