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{{Coexpression_clusters
{
|full_id=C336_left_heart_skeletal_breast_lung_mature_adipose
|

Latest revision as of 11:20, 17 September 2013


Full id: C336_left_heart_skeletal_breast_lung_mature_adipose



Phase1 CAGE Peaks

Hg19::chr10:21112200..21112221,-p@chr10:21112200..21112221
-
Hg19::chr11:111781125..111781137,-p@chr11:111781125..111781137
-
Hg19::chr12:111348835..111348847,-p@chr12:111348835..111348847
-
Hg19::chr12:56091538..56091540,-p@chr12:56091538..56091540
-
Hg19::chr14:23886391..23886400,-p@chr14:23886391..23886400
-
Hg19::chr14:23893155..23893171,-p7@MYH7
Hg19::chr15:36887069..36887086,+p3@C15orf41
Hg19::chr15:63353097..63353109,+p16@TPM1
Hg19::chr19:2273037..2273052,+p@chr19:2273037..2273052
+
Hg19::chr1:145441220..145441237,+p@chr1:145441220..145441237
+
Hg19::chr1:145441715..145441724,+p@chr1:145441715..145441724
+
Hg19::chr1:16342059..16342090,+p@chr1:16342059..16342090
+
Hg19::chr20:62120363..62120378,-p@chr20:62120363..62120378
-
Hg19::chr22:36003307..36003317,-p@chr22:36003307..36003317
-
Hg19::chr2:26467557..26467568,-p3@HADHA
Hg19::chr2:26467825..26467841,+p2@HADHB
Hg19::chr3:37061825..37061832,+p@chr3:37061825..37061832
+
Hg19::chr3:46902281..46902288,-p@chr3:46902281..46902288
-
Hg19::chr3:96337038..96337083,-p@chr3:96337038..96337083
-
Hg19::chr4:186066197..186066221,+p@chr4:186066197..186066221
+
Hg19::chr5:79030927..79030935,+p49@CMYA5
Hg19::chr5:79946820..79946857,-p2@MTRNR2L2
Hg19::chr5:80555040..80555044,+p@chr5:80555040..80555044
+
Hg19::chr6:123760865..123760870,+p5@ENST00000427828
p5@ENST00000434768
Hg19::chr6:140400645..140400650,+p@chr6:140400645..140400650
+
Hg19::chr6:56323932..56323936,-p67@DST
Hg19::chr7:148638575..148638586,+p2@RNY5
Hg19::chr7:32110543..32110557,-p11@PDE1C
Hg19::chr7:80231530..80231551,+p8@CD36
Hg19::chr7:80231563..80231585,+p6@CD36
Hg19::chr7:80231609..80231627,+p11@CD36
Hg19::chr7:95221375..95221386,-p@chr7:95221375..95221386
-
Hg19::chr8:23584449..23584459,-p@chr8:23584449..23584459
-
Hg19::chrX:5225192..5225203,-p1@ENST00000434972


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
3.08914508387101e-060.0019554288380903528Fatty acid elongation in mitochondria (KEGG):00062
0.0001036691831660520.0164056482360278244Fatty acid metabolism (KEGG):00071
0.0001036691831660520.0164056482360278244Valine, leucine and isoleucine degradation (KEGG):00280
0.0003186796600485180.0390577663331827277Cardiac muscle contraction (KEGG):04260
0.0003702157946273240.0390577663331827283Hypertrophic cardiomyopathy (HCM) (KEGG):05410
0.0004351382929817470.0393489342082066290Dilated cardiomyopathy (KEGG):05414
6.15932363774147e-050.0164056482360278234Fatty Acid Beta Oxidation (Wikipathways):WP143



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:0003988acetyl-CoA C-acyltransferase activity6.92129505418527e-05
GO:0004300enoyl-CoA hydratase activity6.92129505418527e-05
GO:00038573-hydroxyacyl-CoA dehydrogenase activity6.92129505418527e-05
GO:0016408C-acyltransferase activity0.000228214532956531
GO:0006635fatty acid beta-oxidation0.00052500760191928
GO:0006631fatty acid metabolic process0.000530362812756355
GO:0019395fatty acid oxidation0.000800337080983666
GO:0032787monocarboxylic acid metabolic process0.00118596621311143
GO:0008016regulation of heart contraction0.00118596621311143
GO:0008307structural constituent of muscle0.00118596621311143
GO:0003015heart process0.00119419938607684
GO:0060047heart contraction0.00119419938607684
GO:0030017sarcomere0.00119419938607684
GO:0030016myofibril0.00135373569175321
GO:0044449contractile fiber part0.00162135059197157
GO:0043292contractile fiber0.00173032124461943
GO:0003779actin binding0.00220390170700477
GO:0016836hydro-lyase activity0.00280062572538729
GO:0016508long-chain-enoyl-CoA hydratase activity0.00280062572538729
GO:0016507fatty acid beta-oxidation multienzyme complex0.00280062572538729
GO:0016509long-chain-3-hydroxyacyl-CoA dehydrogenase activity0.00280062572538729
GO:0016835carbon-oxygen lyase activity0.00313629135527366
GO:0008092cytoskeletal protein binding0.00416575764242442
GO:0005516calmodulin binding0.00509004928055831
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.00509004928055831
GO:0008015blood circulation0.00509004928055831
GO:0003013circulatory system process0.00509004928055831
GO:0006200ATP catabolic process0.00509004928055831
GO:0009207purine ribonucleoside triphosphate catabolic process0.00509004928055831
GO:0009146purine nucleoside triphosphate catabolic process0.00509004928055831
GO:0004117calmodulin-dependent cyclic-nucleotide phosphodiesterase activity0.00509004928055831
GO:0003985acetyl-CoA C-acetyltransferase activity0.00509004928055831
GO:0009203ribonucleoside triphosphate catabolic process0.00509004928055831
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.00509004928055831
GO:0003012muscle system process0.00509004928055831
GO:0006936muscle contraction0.00509004928055831
GO:0044255cellular lipid metabolic process0.00523876299108885
GO:0019752carboxylic acid metabolic process0.00534476070800211
GO:0006082organic acid metabolic process0.00534476070800211
GO:0009154purine ribonucleotide catabolic process0.00534476070800211
GO:0009143nucleoside triphosphate catabolic process0.00534476070800211
GO:0006195purine nucleotide catabolic process0.00534476070800211
GO:0005862muscle thin filament tropomyosin0.00534476070800211
GO:0030898actin-dependent ATPase activity0.00534476070800211
GO:0016453C-acetyltransferase activity0.00625377080234083
GO:0033275actin-myosin filament sliding0.00625377080234083
GO:0030049muscle filament sliding0.00625377080234083
GO:0009261ribonucleotide catabolic process0.00707946691661464
GO:0002027regulation of heart rate0.00707946691661464
GO:0006629lipid metabolic process0.00707946691661464
GO:0055010ventricular cardiac muscle morphogenesis0.00777643195140338
GO:0007512adult heart development0.00777643195140338
GO:0008415acyltransferase activity0.00777643195140338
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.00777643195140338
GO:0005515protein binding0.00788231127580342
GO:0048644muscle morphogenesis0.00824767501883972
GO:0055008cardiac muscle morphogensis0.00824767501883972
GO:0051239regulation of multicellular organismal process0.0087020181146306
GO:0016829lyase activity0.0087020181146306
GO:0015629actin cytoskeleton0.00952041531412415
GO:0016746transferase activity, transferring acyl groups0.00952041531412415
GO:0005865striated muscle thin filament0.01028524455451
GO:0005743mitochondrial inner membrane0.01028524455451
GO:0019866organelle inner membrane0.0112964660841367
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.012648071284402
GO:0045103intermediate filament-based process0.0131454347830111
GO:0000146microfilament motor activity0.0131454347830111
GO:0030048actin filament-based movement0.0134192831021231
GO:0032982myosin filament0.0134192831021231
GO:0005863striated muscle thick filament0.0134192831021231
GO:0031966mitochondrial membrane0.0153170358144426
GO:0005856cytoskeleton0.0155226771801919
GO:0000062acyl-CoA binding0.0160771851772659
GO:0005740mitochondrial envelope0.016423777393706
GO:0005859muscle myosin complex0.0192918421568587
GO:0009166nucleotide catabolic process0.0192918421568587
GO:0016460myosin II complex0.0198006200548218
GO:0000302response to reactive oxygen species0.0202961757118159
GO:0005504fatty acid binding0.0229972128803536
GO:0006941striated muscle contraction0.0269794578053047
GO:0044429mitochondrial part0.0269794578053047
GO:0042221response to chemical stimulus0.0269794578053047
GO:0006937regulation of muscle contraction0.0275117531679227
GO:0031967organelle envelope0.0290746276768742
GO:0031975envelope0.0290746276768742
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0306153492651917
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0316010541811552
GO:0007010cytoskeleton organization and biogenesis0.0336575397112977
GO:0044446intracellular organelle part0.0404207849669413
GO:0044422organelle part0.0404207849669413
GO:0042493response to drug0.0404207849669413
GO:0051287NAD binding0.0456447248263079



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
adult organism5.66e-29114
cardiac chamber1.20e-243
valve2.86e-243
cardiac mesenchyme2.86e-243
cardial valve2.86e-243
tunica intima2.86e-243
heart layer2.86e-243
endocardium2.86e-243
endocardial cushion2.86e-243
presumptive endocardium2.86e-243
primary circulatory organ1.69e-2227
compound organ7.45e-2068
cardiac atrium6.75e-172
future cardiac atrium6.75e-172
muscle structure7.90e-172
muscle organ7.90e-172
atrioventricular valve1.08e-162
heart1.87e-1124
primitive heart tube1.87e-1124
primary heart field1.87e-1124
anterior lateral plate mesoderm1.87e-1124
heart tube1.87e-1124
heart primordium1.87e-1124
cardiac mesoderm1.87e-1124
cardiogenic plate1.87e-1124
heart rudiment1.87e-1124
tongue3.42e-113
gustatory system3.42e-113
future tongue3.42e-113
blood vessel layer9.99e-117
heart left ventricle1.60e-091
cardiac ventricle1.60e-091
future cardiac ventricle1.60e-091
left cardiac atrium1.89e-091
hindlimb bud2.04e-091
soleus muscle2.04e-091
appendage2.04e-091
lower limb segment2.04e-091
multi-limb segment region2.04e-091
hindlimb muscle2.04e-091
hindlimb zeugopod muscle2.04e-091
paired limb/fin2.04e-091
limb2.04e-091
pelvic appendage2.04e-091
limb segment2.04e-091
paired limb/fin segment2.04e-091
limb muscle2.04e-091
pelvic complex muscle2.04e-091
zeugopod2.04e-091
muscle of leg2.04e-091
paired limb/fin bud2.04e-091
limb bud2.04e-091
pelvic appendage bud2.04e-091
limb/fin field2.04e-091
subdivision of organism along appendicular axis2.04e-091
appendage girdle complex2.04e-091
leg2.04e-091
hindlimb2.04e-091
triceps surae2.04e-091
hindlimb zeugopod2.04e-091
posterior region of body2.04e-091
pelvic complex2.04e-091
limb field2.04e-091
hindlimb/pelvic fin field2.04e-091
pulmonary valve2.40e-091
semi-lunar valve2.40e-091
mitral valve3.05e-091
tricuspid valve3.58e-091
right atrium valve3.58e-091
outflow tract of atrium3.58e-091
outflow part of right atrium3.58e-091
right cardiac atrium3.58e-091
chest muscle3.88e-091
respiratory system muscle3.88e-091
skeletal muscle of trunk3.88e-091
respiratory system skeletal muscle3.88e-091
thoracic segment muscle3.88e-091
chest organ3.88e-091
muscle of trunk3.88e-091
diaphragm3.88e-091
future diaphragm3.88e-091
penis4.19e-091
intromittent organ4.19e-091
lateral plate mesenchyme4.19e-091
undifferentiated genital tubercle4.19e-091
somatopleure4.19e-091
epididymis1.16e-081
neural crest-derived structure1.20e-0710
neural crest1.20e-0710
neural fold1.20e-0710
Disease
Ontology termp-valuen
heart disease6.23e-172
vascular disease2.82e-091
ischemia2.82e-091
extrinsic cardiomyopathy2.82e-091
myocardial ischemia2.82e-091
myocardial infarction2.82e-091
cardiovascular system disease6.48e-094


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)
MA0003.10.0478156
MA0004.10.262334
MA0006.10.100229
MA0007.10.515741
MA0009.10.375925
MA0014.10.00846735
MA0017.10.904952
MA0019.10.151679
MA0024.10.294311
MA0025.10.487069
MA0027.11.90579
MA0028.10.273688
MA0029.10.308904
MA0030.10.300221
MA0031.10.703934
MA0038.10.126016
MA0040.10.313366
MA0041.10.0839596
MA0042.10.070122
MA0043.10.376179
MA0046.10.367181
MA0048.10.164128
MA0050.10.528958
MA0051.10.78189
MA0052.10.848544
MA0055.10.0106179
MA0056.10
MA0057.10.0792479
MA0058.10.0404315
MA0059.10.156159
MA0060.10.088709
MA0061.10.144596
MA0063.10
MA0066.10.126249
MA0067.10.649823
MA0068.10.302496
MA0069.10.364099
MA0070.10.355189
MA0071.10.105665
MA0072.10.351626
MA0073.10.0336902
MA0074.10.123313
MA0076.10.173334
MA0077.10.345539
MA0078.10.537126
MA0081.10.156318
MA0083.10.381987
MA0084.10.823032
MA0087.10.349692
MA0088.10.162232
MA0089.10
MA0090.10.0504181
MA0091.14.67545
MA0092.10.221134
MA0093.10.102646
MA0095.10
MA0098.10
MA0100.10.133688
MA0101.10.105302
MA0103.10.440826
MA0105.10.0266755
MA0106.10.14939
MA0107.10.147251
MA0108.20.69888
MA0109.10
MA0111.10.055257
MA0113.10.480586
MA0114.10.750855
MA0115.10.581155
MA0116.10.306176
MA0117.10.406527
MA0119.10.0352635
MA0122.10.42795
MA0124.10.544476
MA0125.10.471774
MA0130.10
MA0131.10.565286
MA0132.10
MA0133.10
MA0135.10.400588
MA0136.10.129893
MA0139.10.0163043
MA0140.10.104326
MA0141.10.637869
MA0142.10.230443
MA0143.12.13898
MA0144.10.443601
MA0145.10.12156
MA0146.10.000772138
MA0147.10.058287
MA0148.11.52127
MA0149.10.0995233
MA0062.20.0589056
MA0035.20.339371
MA0039.20.0486388
MA0138.20.183007
MA0002.20.0772163
MA0137.20.526676
MA0104.20.0879339
MA0047.20.862783
MA0112.20.399857
MA0065.20.211429
MA0150.10.0483839
MA0151.10
MA0152.10.70943
MA0153.11.15826
MA0154.10.633854
MA0155.10.247958
MA0156.10.120803
MA0157.10.211768
MA0158.10
MA0159.11.13838
MA0160.10.0939956
MA0161.10
MA0162.10.0836811
MA0163.10.0612281
MA0164.10.499229
MA0080.20.102716
MA0018.20.45833
MA0099.20.107829
MA0079.20.000750601
MA0102.20.858102
MA0258.10.643532
MA0259.10.0634142
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
ESRRA#2101228.46119494918390.002287760748248220.0129839933043308



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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