Coexpression cluster:C1113

Full id: C1113_heart_skeletal_smooth_bladder_penis_tongue_diaphragm

Phase1 CAGE Peaks

Hg19::chr10:29923874..29923879,-	p12@SVIL
Hg19::chr22:36291022..36291026,-	p@chr22:36291022..36291026 -
Hg19::chr6:76203489..76203522,-	p1@FILIP1
Hg19::chrX:33229600..33229611,-	p7@DMD
Hg19::chrX:33229614..33229635,-	p3@DMD
Hg19::chrX:33229636..33229651,-	p4@DMD
Hg19::chrX:33229657..33229675,-	p2@DMD

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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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

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GO ID	GO name	FDR corrected p-value
GO:0043034	costamere	9.77416470118443e-07
GO:0030016	myofibril	8.2102983489949e-05
GO:0044449	contractile fiber part	8.2102983489949e-05
GO:0043292	contractile fiber	8.2102983489949e-05
GO:0007517	muscle development	0.00047912955365206
GO:0003779	actin binding	0.00259838023443736
GO:0043043	peptide biosynthetic process	0.00369591711616474
GO:0008092	cytoskeletal protein binding	0.00369591711616474
GO:0048513	organ development	0.00848267173866793
GO:0051693	actin filament capping	0.00848267173866793
GO:0051016	barbed-end actin filament capping	0.00848267173866793
GO:0030835	negative regulation of actin filament depolymerization	0.00848267173866793
GO:0016010	dystrophin-associated glycoprotein complex	0.00848267173866793
GO:0030834	regulation of actin filament depolymerization	0.00848267173866793
GO:0030042	actin filament depolymerization	0.00848267173866793
GO:0006518	peptide metabolic process	0.00961264662949734
GO:0005856	cytoskeleton	0.00961264662949734
GO:0005509	calcium ion binding	0.00961264662949734
GO:0048731	system development	0.00962668341602653
GO:0051015	actin filament binding	0.00962668341602653
GO:0005605	basal lamina	0.00962668341602653
GO:0008307	structural constituent of muscle	0.00962668341602653
GO:0008064	regulation of actin polymerization and/or depolymerization	0.00962668341602653
GO:0051261	protein depolymerization	0.00962668341602653
GO:0030832	regulation of actin filament length	0.00962668341602653
GO:0032535	regulation of cellular component size	0.00962668341602653
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.00962668341602653
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0102696566719827
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0103217134077448
GO:0033043	regulation of organelle organization and biogenesis	0.0103217134077448
GO:0048856	anatomical structure development	0.010539812693488
GO:0008154	actin polymerization and/or depolymerization	0.010539812693488
GO:0007519	skeletal muscle development	0.0112247198530957
GO:0005604	basement membrane	0.0120315799077811
GO:0007275	multicellular organismal development	0.0122947402574183
GO:0005200	structural constituent of cytoskeleton	0.0130501615289126
GO:0014706	striated muscle development	0.0131450187455632
GO:0051128	regulation of cellular component organization and biogenesis	0.0145418564873345
GO:0051248	negative regulation of protein metabolic process	0.0147348790925255
GO:0043232	intracellular non-membrane-bound organelle	0.0169329059648885
GO:0043228	non-membrane-bound organelle	0.0169329059648885
GO:0044420	extracellular matrix part	0.0172276867122797
GO:0003012	muscle system process	0.0202706437938474
GO:0006936	muscle contraction	0.0202706437938474
GO:0032502	developmental process	0.0202706437938474
GO:0005886	plasma membrane	0.0253086085924412
GO:0032501	multicellular organismal process	0.0253086085924412
GO:0030036	actin cytoskeleton organization and biogenesis	0.0283737756670157
GO:0030029	actin filament-based process	0.0292519804867804
GO:0015629	actin cytoskeleton	0.0326188506973571
GO:0044444	cytoplasmic part	0.0336695570485764
GO:0005578	proteinaceous extracellular matrix	0.0437898899623931
GO:0051246	regulation of protein metabolic process	0.0437898899623931
GO:0009892	negative regulation of metabolic process	0.0443956015287848

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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
muscle precursor cell	1.75e-09	57
myoblast	1.75e-09	57
multi-potent skeletal muscle stem cell	1.75e-09	57
muscle cell	2.78e-08	54
contractile cell	5.33e-08	59

Uber Anatomy

Ontology term	p-value	n
adult organism	2.56e-41	115
multi-tissue structure	4.44e-18	347
regional part of brain	1.24e-17	59
neural tube	6.28e-17	57
neural rod	6.28e-17	57
future spinal cord	6.28e-17	57
neural keel	6.28e-17	57
anatomical cluster	3.27e-16	286
anatomical conduit	9.49e-16	241
neural plate	8.51e-15	86
presumptive neural plate	8.51e-15	86
cell layer	5.30e-14	312
brain	5.91e-14	69
future brain	5.91e-14	69
epithelium	6.54e-14	309
multi-cellular organism	1.12e-13	659
organism subdivision	1.80e-13	365
neurectoderm	2.68e-13	90
central nervous system	3.19e-13	82
tube	9.69e-13	194
anterior neural tube	1.09e-12	42
muscle tissue	1.34e-12	63
musculature	1.34e-12	63
musculature of body	1.34e-12	63
regional part of forebrain	3.39e-12	41
forebrain	3.39e-12	41
future forebrain	3.39e-12	41
regional part of nervous system	1.28e-11	94
nervous system	1.28e-11	94
skeletal muscle tissue	1.42e-11	61
striated muscle tissue	1.42e-11	61
myotome	1.42e-11	61
anterior region of body	3.35e-10	129
craniocervical region	3.35e-10	129
head	5.17e-10	123
ectoderm-derived structure	6.82e-10	169
gray matter	7.29e-10	34
brain grey matter	7.29e-10	34
anatomical system	7.38e-10	625
telencephalon	9.62e-10	34
anatomical group	1.17e-09	626
embryo	1.28e-09	612
regional part of telencephalon	1.63e-09	33
embryonic structure	2.14e-09	605
developing anatomical structure	2.14e-09	605
ectoderm	3.83e-09	173
presumptive ectoderm	3.83e-09	173
germ layer	4.32e-09	604
embryonic tissue	4.32e-09	604
presumptive structure	4.32e-09	604
epiblast (generic)	4.32e-09	604
cerebral hemisphere	7.24e-09	32
primary circulatory organ	1.09e-08	27
dermomyotome	2.35e-08	70
pre-chordal neural plate	3.17e-08	61
somite	2.07e-07	83
paraxial mesoderm	2.07e-07	83
presomitic mesoderm	2.07e-07	83
presumptive segmental plate	2.07e-07	83
trunk paraxial mesoderm	2.07e-07	83
presumptive paraxial mesoderm	2.07e-07	83
splanchnic layer of lateral plate mesoderm	5.08e-07	84
heart	5.36e-07	24
primitive heart tube	5.36e-07	24
primary heart field	5.36e-07	24
anterior lateral plate mesoderm	5.36e-07	24
heart tube	5.36e-07	24
heart primordium	5.36e-07	24
cardiac mesoderm	5.36e-07	24
cardiogenic plate	5.36e-07	24
heart rudiment	5.36e-07	24
circulatory system	7.29e-07	113

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)
{{{tfbs_overrepresentation_jaspar}}}

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
FOS#2353	4	5.14168874793966	0.00404209586567825	0.0193470417101545
STAT1#6772	4	11.8323357126853	0.000169095029557169	0.00206647739198704
STAT3#6774	6	9.01668428327506	4.74133156431288e-06	0.000147155996209591

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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This analysis result is provided for C0 - C305 clusters.