Coexpression cluster:C20

Full id: C20_heart_left_skeletal_diaphragm_tongue_umbilical_throat

Phase1 CAGE Peaks

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Hg19::chr10:103699708..103699719,-	p@chr10:103699708..103699719 -
Hg19::chr10:103726939..103726956,-	p@chr10:103726939..103726956 -
Hg19::chr10:108408655..108408660,+	p@chr10:108408655..108408660 +
Hg19::chr10:112517795..112517799,+	p@chr10:112517795..112517799 +
Hg19::chr10:112524356..112524374,+	p@chr10:112524356..112524374 +
Hg19::chr10:112572579..112572608,+	p@chr10:112572579..112572608 +
Hg19::chr10:115614503..115614514,+	p4@NHLRC2
Hg19::chr10:115614552..115614563,+	p7@NHLRC2
Hg19::chr10:116391770..116391838,-	p5@ABLIM1
Hg19::chr10:116391923..116392002,-	p7@ABLIM1
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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

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p.value	FDR	nGenes	nPathway	Name
0.000231657192529121	0.0146639002870933	7	177	Calcium signaling pathway (KEGG):04020
6.30934046684172e-15	7.98762503102162e-13	13	77	Cardiac muscle contraction (KEGG):04260
1.66943907379131e-17	5.28377466854948e-15	15	83	Hypertrophic cardiomyopathy (HCM) (KEGG):05410
7.88252100001465e-07	7.12805113287039e-05	7	74	Arrhythmogenic right ventricular cardiomyopathy (ARVC) (KEGG):05412
1.80419036842224e-18	1.14205250321128e-15	16	90	Dilated cardiomyopathy (KEGG):05414
3.3423723116765e-05	0.00264465209161403	4	27	Proteins and DNA Sequences in Cardicac Structures (Wikipathways):WP1550
0.00072677724805668	0.0353884613861445	6	155	Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
2.59780828378785e-17	5.48137547879235e-15	12	39	Striated Muscle Contraction (Wikipathways):WP383
0.000119209861846449	0.00838442694986693	4	37	Sandbox Pathway (Wikipathways):WP4
0.000590865467916936	0.0311681534326184	6	149	Calcium Regulation in the Cardiac Cell (Wikipathways):WP536
1.20381781467267e-12	1.27002779447966e-10	10	49	Muscle contraction (Reactome):REACT_17044
1.05480829310387e-15	1.66923412383687e-13	21	288	{ACTB,297} (Static Module):NA
0.000418496897381243	0.0240825941856661	4	51	{RXRA,51} (Static Module):NA

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

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GO ID	GO name	FDR corrected p-value
GO:0006936	muscle contraction	1.05751769297081e-28
GO:0003012	muscle system process	1.05751769297081e-28
GO:0005856	cytoskeleton	5.44006125812182e-25
GO:0044449	contractile fiber part	2.84073743440755e-21
GO:0030017	sarcomere	3.78895651587484e-21
GO:0043292	contractile fiber	6.07839266221264e-21
GO:0030016	myofibril	1.51424532702748e-20
GO:0008307	structural constituent of muscle	2.53002378767014e-20
GO:0003008	system process	2.75003715235446e-19
GO:0005737	cytoplasm	5.7727270248596e-19
GO:0015629	actin cytoskeleton	2.01291352194336e-17
GO:0060047	heart contraction	6.85273603523471e-16
GO:0003015	heart process	6.85273603523471e-16
GO:0008016	regulation of heart contraction	1.12593579305353e-14
GO:0007517	muscle development	4.26645042493245e-14
GO:0006941	striated muscle contraction	1.72110638760366e-13
GO:0008015	blood circulation	5.8757171663596e-12
GO:0003013	circulatory system process	5.8757171663596e-12
GO:0016528	sarcoplasm	1.95149340125531e-11
GO:0016529	sarcoplasmic reticulum	1.95149340125531e-11
GO:0051239	regulation of multicellular organismal process	5.23736273403332e-11
GO:0032501	multicellular organismal process	6.32133608835853e-11
GO:0008092	cytoskeletal protein binding	2.09546324594442e-10
GO:0044444	cytoplasmic part	2.04736423951825e-09
GO:0055008	cardiac muscle morphogensis	7.20264568812095e-09
GO:0048644	muscle morphogenesis	7.20264568812095e-09
GO:0031674	I band	7.24326329202904e-09
GO:0048513	organ development	1.34792652690571e-08
GO:0043228	non-membrane-bound organelle	1.6548641073336e-08
GO:0043232	intracellular non-membrane-bound organelle	1.6548641073336e-08
GO:0033018	sarcoplasmic reticulum lumen	2.22118958060532e-08
GO:0007507	heart development	4.29565772044466e-08
GO:0044424	intracellular part	5.15478229405041e-08
GO:0005859	muscle myosin complex	7.96110952820054e-08
GO:0016460	myosin II complex	1.0011931345007e-07
GO:0003779	actin binding	2.23959574192018e-07
GO:0005515	protein binding	2.49536222986095e-07
GO:0005863	striated muscle thick filament	3.62514518065399e-07
GO:0032982	myosin filament	3.62514518065399e-07
GO:0055010	ventricular cardiac muscle morphogenesis	5.9541751059795e-07
GO:0044430	cytoskeletal part	1.21011431260716e-06
GO:0016459	myosin complex	1.97354519912282e-06
GO:0005790	smooth endoplasmic reticulum	7.68066500143272e-06
GO:0048856	anatomical structure development	1.3570515009947e-05
GO:0030018	Z disc	1.47253202313085e-05
GO:0005622	intracellular	2.80860364191816e-05
GO:0048731	system development	2.8203127372795e-05
GO:0030049	muscle filament sliding	2.8203127372795e-05
GO:0033275	actin-myosin filament sliding	2.8203127372795e-05
GO:0006937	regulation of muscle contraction	3.3938835292669e-05
GO:0005861	troponin complex	5.39933143552282e-05
GO:0043229	intracellular organelle	6.42149723950858e-05
GO:0005887	integral to plasma membrane	6.42149723950858e-05
GO:0043226	organelle	6.42149723950858e-05
GO:0000267	cell fraction	6.8368456546819e-05
GO:0044446	intracellular organelle part	6.8368456546819e-05
GO:0044464	cell part	6.8368456546819e-05
GO:0044422	organelle part	7.19920293628092e-05
GO:0031226	intrinsic to plasma membrane	7.65239996744321e-05
GO:0048738	cardiac muscle development	7.74361416271956e-05
GO:0007512	adult heart development	7.74361416271956e-05
GO:0002026	regulation of the force of heart contraction	7.74361416271956e-05
GO:0014706	striated muscle development	0.000101166974930067
GO:0005624	membrane fraction	0.000179457571512481
GO:0005865	striated muscle thin filament	0.000343075984136097
GO:0007275	multicellular organismal development	0.000358278264091356
GO:0031013	troponin I binding	0.000411548223425469
GO:0031014	troponin T binding	0.000411548223425469
GO:0030048	actin filament-based movement	0.00106134952044451
GO:0051146	striated muscle cell differentiation	0.00106134952044451
GO:0045822	negative regulation of heart contraction	0.00116218590675779
GO:0030172	troponin C binding	0.00116218590675779
GO:0005516	calmodulin binding	0.00126742539320808
GO:0005509	calcium ion binding	0.00181986295583941
GO:0004111	creatine kinase activity	0.00219473594335477
GO:0030898	actin-dependent ATPase activity	0.00219473594335477
GO:0032502	developmental process	0.00236126936422951
GO:0042805	actinin binding	0.00355228953842855
GO:0005788	endoplasmic reticulum lumen	0.00427165065362383
GO:0006874	cellular calcium ion homeostasis	0.00427165065362383
GO:0055074	calcium ion homeostasis	0.00427165065362383
GO:0030029	actin filament-based process	0.00493144102952482
GO:0007519	skeletal muscle development	0.00493144102952482
GO:0002027	regulation of heart rate	0.00493144102952482
GO:0006875	cellular metal ion homeostasis	0.00526909936175276
GO:0055065	metal ion homeostasis	0.00526909936175276
GO:0043167	ion binding	0.00572324197977719
GO:0006512	ubiquitin cycle	0.00626802957935771
GO:0030371	translation repressor activity	0.00626993202379179
GO:0055002	striated muscle cell development	0.00626993202379179
GO:0030239	myofibril assembly	0.00626993202379179
GO:0055001	muscle cell development	0.00626993202379179
GO:0009887	organ morphogenesis	0.00626993202379179
GO:0035051	cardiac cell differentiation	0.00808566665778536
GO:0006942	regulation of striated muscle contraction	0.00808566665778536
GO:0005739	mitochondrion	0.00819043501349864
GO:0007010	cytoskeleton organization and biogenesis	0.00862774828988738
GO:0044459	plasma membrane part	0.00863462056629045
GO:0033017	sarcoplasmic reticulum membrane	0.0122635369189636
GO:0048628	myoblast maturation	0.0122635369189636
GO:0009653	anatomical structure morphogenesis	0.0143858696676094
GO:0048627	myoblast development	0.0143858696676094
GO:0005246	calcium channel regulator activity	0.0143858696676094
GO:0044432	endoplasmic reticulum part	0.0143858696676094
GO:0042692	muscle cell differentiation	0.0171687207048302
GO:0046872	metal ion binding	0.0224249166413304
GO:0005783	endoplasmic reticulum	0.0229890056251833
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0229890056251833
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.024467576897517
GO:0000146	microfilament motor activity	0.0255867087129621
GO:0065007	biological regulation	0.0266547663341774
GO:0022892	substrate-specific transporter activity	0.0291879065851272
GO:0022857	transmembrane transporter activity	0.0300258334301265
GO:0051789	response to protein stimulus	0.0320049870436943
GO:0006986	response to unfolded protein	0.0320049870436943
GO:0030003	cellular cation homeostasis	0.0336471667869255
GO:0022891	substrate-specific transmembrane transporter activity	0.0341238420811505
GO:0050789	regulation of biological process	0.0341238420811505
GO:0001570	vasculogenesis	0.0341238420811505
GO:0055080	cation homeostasis	0.0346474849856165
GO:0005813	centrosome	0.0380427338720723
GO:0048878	chemical homeostasis	0.0380427338720723
GO:0031967	organelle envelope	0.0380427338720723
GO:0006635	fatty acid beta-oxidation	0.0380427338720723
GO:0031975	envelope	0.0380427338720723
GO:0031966	mitochondrial membrane	0.0380427338720723
GO:0005523	tropomyosin binding	0.0380427338720723
GO:0031032	actomyosin structure organization and biogenesis	0.0380427338720723
GO:0046314	phosphocreatine biosynthetic process	0.0380427338720723
GO:0051370	ZASP binding	0.0380427338720723
GO:0005477	pyruvate secondary active transmembrane transporter activity	0.0380427338720723
GO:0055013	cardiac muscle cell development	0.0380427338720723
GO:0006848	pyruvate transport	0.0380427338720723
GO:0050080	malonyl-CoA decarboxylase activity	0.0380427338720723
GO:0051374	FATZ 1 binding	0.0380427338720723
GO:0043033	isoamylase complex	0.0380427338720723
GO:0032780	negative regulation of ATPase activity	0.0380427338720723
GO:0004492	methylmalonyl-CoA decarboxylase activity	0.0380427338720723
GO:0055003	cardiac myofibril assembly	0.0380427338720723
GO:0060044	negative regulation of cardiac muscle cell proliferation	0.0380427338720723
GO:0055009	atrial cardiac muscle morphogenesis	0.0380427338720723
GO:0015866	ADP transport	0.0380427338720723
GO:0001980	ischemic regulation of systemic arterial blood pressure	0.0380427338720723
GO:0060039	pericardium development	0.0380427338720723
GO:0006603	phosphocreatine metabolic process	0.0380427338720723
GO:0050833	pyruvate transmembrane transporter activity	0.0380427338720723
GO:0008267	poly-glutamine tract binding	0.0380427338720723
GO:0015085	calcium ion transmembrane transporter activity	0.0446282503028984
GO:0005740	mitochondrial envelope	0.0482474283684438
GO:0005815	microtubule organizing center	0.0490762999901469

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>

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Uber Anatomy

Ontology term	p-value	n
cardiac chamber	2.64e-24	3
valve	3.62e-24	3
cardiac mesenchyme	3.62e-24	3
cardial valve	3.62e-24	3
tunica intima	3.62e-24	3
heart layer	3.62e-24	3
endocardium	3.62e-24	3
endocardial cushion	3.62e-24	3
presumptive endocardium	3.62e-24	3
primary circulatory organ	1.60e-22	27
compound organ	4.16e-17	68
muscle structure	1.17e-16	2
muscle organ	1.17e-16	2
cardiac atrium	1.37e-16	2
future cardiac atrium	1.37e-16	2
atrioventricular valve	1.60e-16	2
adult organism	1.66e-16	114
throat	3.49e-16	2
heart	2.02e-11	24
primitive heart tube	2.02e-11	24
primary heart field	2.02e-11	24
anterior lateral plate mesoderm	2.02e-11	24
heart tube	2.02e-11	24
heart primordium	2.02e-11	24
cardiac mesoderm	2.02e-11	24
cardiogenic plate	2.02e-11	24
heart rudiment	2.02e-11	24
tongue	3.09e-11	3
gustatory system	3.09e-11	3
future tongue	3.09e-11	3
blood vessel layer	1.10e-10	7
heart left ventricle	1.74e-09	1
cardiac ventricle	1.74e-09	1
future cardiac ventricle	1.74e-09	1
pulmonary valve	2.04e-09	1
semi-lunar valve	2.04e-09	1
left cardiac atrium	2.40e-09	1
mitral valve	2.82e-09	1
hindlimb bud	3.05e-09	1
soleus muscle	3.05e-09	1
appendage	3.05e-09	1
lower limb segment	3.05e-09	1
multi-limb segment region	3.05e-09	1
hindlimb muscle	3.05e-09	1
hindlimb zeugopod muscle	3.05e-09	1
paired limb/fin	3.05e-09	1
limb	3.05e-09	1
pelvic appendage	3.05e-09	1
limb segment	3.05e-09	1
paired limb/fin segment	3.05e-09	1
limb muscle	3.05e-09	1
pelvic complex muscle	3.05e-09	1
zeugopod	3.05e-09	1
muscle of leg	3.05e-09	1
paired limb/fin bud	3.05e-09	1
limb bud	3.05e-09	1
pelvic appendage bud	3.05e-09	1
limb/fin field	3.05e-09	1
subdivision of organism along appendicular axis	3.05e-09	1
appendage girdle complex	3.05e-09	1
leg	3.05e-09	1
hindlimb	3.05e-09	1
triceps surae	3.05e-09	1
hindlimb zeugopod	3.05e-09	1
posterior region of body	3.05e-09	1
pelvic complex	3.05e-09	1
limb field	3.05e-09	1
hindlimb/pelvic fin field	3.05e-09	1
chest muscle	3.88e-09	1
respiratory system muscle	3.88e-09	1
skeletal muscle of trunk	3.88e-09	1
respiratory system skeletal muscle	3.88e-09	1
thoracic segment muscle	3.88e-09	1
chest organ	3.88e-09	1
muscle of trunk	3.88e-09	1
diaphragm	3.88e-09	1
future diaphragm	3.88e-09	1
penis	4.54e-09	1
intromittent organ	4.54e-09	1
lateral plate mesenchyme	4.54e-09	1
undifferentiated genital tubercle	4.54e-09	1
somatopleure	4.54e-09	1
tricuspid valve	5.75e-09	1
right atrium valve	5.75e-09	1
outflow tract of atrium	5.75e-09	1
outflow part of right atrium	5.75e-09	1
right cardiac atrium	5.75e-09	1
surface	6.72e-09	1
epididymis	9.91e-09	1
tonsil	1.16e-08	1
mucosa-associated lymphoid tissue	1.16e-08	1
lymphoid tissue	1.16e-08	1
tonsillar ring	1.16e-08	1
neural crest-derived structure	1.28e-07	10
neural crest	1.28e-07	10
neural fold	1.28e-07	10
chordate pharynx	2.29e-07	10
pharyngeal region of foregut	2.29e-07	10
pharynx	9.76e-07	11

Disease

Ontology term	p-value	n
heart disease	3.57e-17	2

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

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
MA0003.1	3.16102e-07
MA0004.1	0.00732709
MA0006.1	0.026212
MA0007.1	1.00461
MA0009.1	0.101935
MA0014.1	1.39894e-05
MA0017.1	4.09165
MA0019.1	0.140325
MA0024.1	0.0898518
MA0025.1	0.00965068
MA0027.1	0.607113
MA0028.1	1.40492e-05
MA0029.1	1.00999
MA0030.1	0.0646121
MA0031.1	0.17127
MA0038.1	8.10445e-05
MA0040.1	0.00739384
MA0041.1	0.0815894
MA0042.1	0.384212
MA0043.1	0.00251651
MA0046.1	0.000560894
MA0048.1	1.244
MA0050.1	0.000131508
MA0051.1	0.0203215
MA0052.1	30.5283
MA0055.1	6.7733
MA0056.1	0
MA0057.1	0.36407
MA0058.1	0.000423746
MA0059.1	0.0322873
MA0060.1	0.000881627
MA0061.1	0.000589625
MA0063.1	0
MA0066.1	0.473586
MA0067.1	0.166769
MA0068.1	0.0412546
MA0069.1	1.191
MA0070.1	0.913245
MA0071.1	5.50911
MA0072.1	0.56869
MA0073.1	7.91932e-07
MA0074.1	1.99354
MA0076.1	1.79514e-06
MA0077.1	0.531085
MA0078.1	0.257538
MA0081.1	0.0897055
MA0083.1	2.75288
MA0084.1	0.146139
MA0087.1	0.0366158
MA0088.1	0.040391
MA0089.1	0
MA0090.1	3.77681
MA0091.1	2.4356
MA0092.1	0.685505
MA0093.1	0.0014941
MA0095.1	0
MA0098.1	0
MA0100.1	2.50375e-05
MA0101.1	0.0115424
MA0103.1	2.17796
MA0105.1	0.0146301
MA0106.1	0.278227
MA0107.1	5.75693e-05
MA0108.2	5.23897
MA0109.1	0
MA0111.1	0.828817
MA0113.1	2.39527
MA0114.1	8.15082
MA0115.1	5.43268
MA0116.1	3.49362
MA0117.1	0.959639
MA0119.1	1.17095
MA0122.1	1.89639
MA0124.1	0.0568876
MA0125.1	0.0196837
MA0130.1	0
MA0131.1	0.0017333
MA0132.1	0
MA0133.1	0
MA0135.1	0.913134
MA0136.1	0.000115637
MA0139.1	0.139522
MA0140.1	0.856981
MA0141.1	23.3303
MA0142.1	0.000827091
MA0143.1	0.0713619
MA0144.1	0.0674293
MA0145.1	1.67354
MA0146.1	0.89167
MA0147.1	2.75282e-05
MA0148.1	0.0738486
MA0149.1	10.0864
MA0062.2	4.31585e-12
MA0035.2	3.83548
MA0039.2	1.84008e-10
MA0138.2	2.68723
MA0002.2	0.00132694
MA0137.2	0.355827
MA0104.2	1.41945e-06
MA0047.2	0.134761
MA0112.2	8.31166
MA0065.2	10.6775
MA0150.1	0.28132
MA0151.1	0
MA0152.1	0.0735245
MA0153.1	0.0351097
MA0154.1	3.38074
MA0155.1	2.59831
MA0156.1	6.38608e-10
MA0157.1	0.176996
MA0158.1	0
MA0159.1	9.80254
MA0160.1	10.1656
MA0161.1	0
MA0162.1	0
MA0163.1	0.000397121
MA0164.1	0.0294605
MA0080.2	7.42216e-06
MA0018.2	0.0714354
MA0099.2	3.05849e-05
MA0079.2	7.41131e-11
MA0102.2	0.0696224
MA0258.1	8.91533
MA0259.1	0.00602468
MA0442.1	0

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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ZNF274#10782	5	9.2082004782782	0.000233591262925649	0.00256611317015797

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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FF samples	Score

FF samples	Score
heart, adult, diseased, donor1 CNhs11758	1.20
left ventricle, adult, donor1 CNhs11789	0.98
heart, adult, pool1 CNhs10621	0.85
heart - pulmonic valve, adult CNhs12856	0.80
heart, adult, diseased post-infarction, donor1 CNhs11757	0.79
left atrium, adult, donor1 CNhs11790	0.72
heart, fetal, pool1 CNhs10653	0.63
heart - mitral valve, adult CNhs12855	0.58
skeletal muscle - soleus muscle, donor1 CNhs13454	0.56
umbilical cord, fetal, donor1 CNhs11765	0.52

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