Coexpression cluster:C193

Full id: C193_Mesenchymal_Adipocyte_mature_Cardiac_heart_CD14CD16_CD14

Phase1 CAGE Peaks

Hg19::chr10:105211353..105211386,-	p4@CALHM2
Hg19::chr10:73047521..73047525,+	p@chr10:73047521..73047525 +
Hg19::chr10:99123608..99123611,-	p4@RRP12
Hg19::chr11:113930128..113930159,-	p@chr11:113930128..113930159 -
Hg19::chr11:114050496..114050536,+	p@chr11:114050496..114050536 +
Hg19::chr11:3078838..3078876,-	p6@CARS
Hg19::chr11:67134927..67134931,-	p@chr11:67134927..67134931 -
Hg19::chr11:7687678..7687681,-	p@chr11:7687678..7687681 -
Hg19::chr11:9781782..9781788,-	p@chr11:9781782..9781788 -
Hg19::chr12:53455252..53455256,+	p9@TENC1
Hg19::chr14:105818803..105818808,+	p@chr14:105818803..105818808 +
Hg19::chr15:35731807..35731812,+	p@chr15:35731807..35731812 +
Hg19::chr15:64448917..64448928,-	p@chr15:64448917..64448928 -
Hg19::chr15:90328175..90328186,-	p@chr15:90328175..90328186 -
Hg19::chr15:90344339..90344342,-	p@chr15:90344339..90344342 -
Hg19::chr16:2819861..2819890,+	p@chr16:2819861..2819890 +
Hg19::chr16:30662360..30662387,+	p7@PRR14
Hg19::chr16:67701309..67701312,-	p@chr16:67701309..67701312 -
Hg19::chr16:86797626..86797635,-	p@chr16:86797626..86797635 -
Hg19::chr16:89595986..89595990,+	p@chr16:89595986..89595990 +
Hg19::chr16:89628797..89628803,+	p3@RPL13
Hg19::chr17:27894290..27894311,+	p@chr17:27894290..27894311 +
Hg19::chr17:36862346..36862379,-	p@chr17:36862346..36862379 -
Hg19::chr17:43013396..43013400,-	p2@KIF18B
Hg19::chr17:61571793..61571795,+	p@chr17:61571793..61571795 +
Hg19::chr17:79204340..79204344,-	p@chr17:79204340..79204344 -
Hg19::chr19:11217362..11217367,+	p6@LDLR
Hg19::chr19:17378331..17378339,+	p3@BABAM1
Hg19::chr19:3620703..3620705,-	p2@C19orf29
Hg19::chr19:36239576..36239581,+	p6@LIN37
Hg19::chr19:45409274..45409280,+	p6@APOE
Hg19::chr19:46894342..46894354,+	p@chr19:46894342..46894354 +
Hg19::chr19:47778119..47778195,+	p1@PRR24
Hg19::chr19:49977466..49977514,+	p2@FLT3LG
Hg19::chr19:50143452..50143468,-	p2@RRAS
Hg19::chr19:52097813..52097865,+	p@chr19:52097813..52097865 +
Hg19::chr19:55758241..55758245,-	p11@PPP6R1
Hg19::chr19:58987786..58987805,+	p3@ZNF446
Hg19::chr19:7584815..7584829,+	p2@ZNF358
Hg19::chr19:850817..850829,+	p@chr19:850817..850829 +
Hg19::chr19:850985..851002,+	p@chr19:850985..851002 +
Hg19::chr19:8590447..8590459,-	p@chr19:8590447..8590459 -
Hg19::chr19:859425..859481,+	p2@CFD
Hg19::chr19:859654..859672,+	p1@CFD
Hg19::chr1:145556687..145556690,+	p@chr1:145556687..145556690 +
Hg19::chr1:27269555..27269558,+	p@chr1:27269555..27269558 +
Hg19::chr1:33834133..33834136,-	p@chr1:33834133..33834136 -
Hg19::chr20:62293295..62293299,+	p@chr20:62293295..62293299 +
Hg19::chr20:62371206..62371224,+	p6@SLC2A4RG
Hg19::chr21:46386905..46386944,+	p@chr21:46386905..46386944 +
Hg19::chr21:47423384..47423395,+	p@chr21:47423384..47423395 +
Hg19::chr21:47680704..47680707,-	p@chr21:47680704..47680707 -
Hg19::chr22:24577444..24577465,+	p1@SUSD2
Hg19::chr22:24581731..24581748,+	p@chr22:24581731..24581748 +
Hg19::chr22:24584625..24584636,+	p@chr22:24584625..24584636 +
Hg19::chr22:45898503..45898514,+	p11@FBLN1
Hg19::chr22:45898527..45898538,+	p7@FBLN1
Hg19::chr22:46493889..46493892,+	p@chr22:46493889..46493892 +
Hg19::chr3:10359730..10359734,-	p4@SEC13
Hg19::chr3:45067642..45067645,+	p7@CLEC3B
Hg19::chr3:52029054..52029058,-	p@chr3:52029054..52029058 -
Hg19::chr3:9920487..9920502,-	p2@CIDEC
Hg19::chr3:9920507..9920519,-	p4@CIDEC
Hg19::chr3:9920535..9920548,-	p3@CIDEC
Hg19::chr3:9956869..9956894,+	p@chr3:9956869..9956894 +
Hg19::chr3:9956901..9956922,+	p@chr3:9956901..9956922 +
Hg19::chr3:9956948..9956961,+	p@chr3:9956948..9956961 +
Hg19::chr3:9958774..9958848,+	p1@IL17RC
Hg19::chr3:9958849..9958863,+	p2@IL17RC
Hg19::chr3:9958870..9958879,+	p3@IL17RC
Hg19::chr4:5798958..5798961,+	p@chr4:5798958..5798961 +
Hg19::chr4:891819..891820,-	p@chr4:891819..891820 -
Hg19::chr5:149425247..149425250,+	p@chr5:149425247..149425250 +
Hg19::chr6:31763316..31763327,-	p7@VARS
Hg19::chr7:100201583..100201598,+	p18@PCOLCE
Hg19::chr7:150711272..150711306,-	p8@ATG9B
Hg19::chr7:150775644..150775650,-	p5@FASTK
Hg19::chr8:143751707..143751730,+	p2@PSCA
Hg19::chr8:21990868..21990906,-	p2@HR
Hg19::chr8:22409352..22409361,+	p24@SORBS3
Hg19::chr9:117004510..117004513,+	p@chr9:117004510..117004513 +
Hg19::chr9:131903916..131903951,+	p8@PPP2R4
Hg19::chr9:134165195..134165202,+	p5@PPAPDC3
Hg19::chr9:139282891..139282896,-	p@chr9:139282891..139282896 -
Hg19::chr9:21994750..21994776,-	p13@CDKN2A
Hg19::chr9:38068437..38068455,-	p3@ENST00000540557
Hg19::chrX:69623884..69623886,+	p@chrX:69623884..69623886 +

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
1.9629592890301e-06	0.00124255322995605	8	740	TGF beta receptor down reg. targets (Netpath):NetPath_7

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:0048518	positive regulation of biological process	0.00140632531219541
GO:0048522	positive regulation of cellular process	0.00388887713003141
GO:0006917	induction of apoptosis	0.00392172611206062
GO:0012502	induction of programmed cell death	0.00392172611206062
GO:0005625	soluble fraction	0.00392172611206062
GO:0045936	negative regulation of phosphate metabolic process	0.00392172611206062
GO:0043065	positive regulation of apoptosis	0.00392172611206062
GO:0043068	positive regulation of programmed cell death	0.00392172611206062
GO:0042632	cholesterol homeostasis	0.00392172611206062
GO:0055092	sterol homeostasis	0.00392172611206062
GO:0055088	lipid homeostasis	0.00438854313126638
GO:0015918	sterol transport	0.00438854313126638
GO:0030301	cholesterol transport	0.00438854313126638
GO:0008034	lipoprotein binding	0.0107484795777597
GO:0065007	biological regulation	0.0178024265771723
GO:0050789	regulation of biological process	0.0191590005068112
GO:0003817	complement factor D activity	0.0191590005068112
GO:0050749	apolipoprotein E receptor binding	0.0191590005068112
GO:0032515	negative regulation of phosphoprotein phosphatase activity	0.0191590005068112
GO:0030229	very-low-density lipoprotein receptor activity	0.0191590005068112
GO:0032516	positive regulation of phosphoprotein phosphatase activity	0.0191590005068112
GO:0035305	negative regulation of dephosphorylation	0.0191590005068112
GO:0035308	negative regulation of protein amino acid dephosphorylation	0.0191590005068112
GO:0042981	regulation of apoptosis	0.0259099367043505
GO:0043067	regulation of programmed cell death	0.0259099367043505
GO:0050794	regulation of cellular process	0.0259099367043505
GO:0051174	regulation of phosphorus metabolic process	0.0259099367043505
GO:0019220	regulation of phosphate metabolic process	0.0259099367043505
GO:0008160	protein tyrosine phosphatase activator activity	0.0259099367043505
GO:0048156	tau protein binding	0.0259099367043505
GO:0035306	positive regulation of dephosphorylation	0.0259099367043505
GO:0035304	regulation of protein amino acid dephosphorylation	0.0259099367043505
GO:0035307	positive regulation of protein amino acid dephosphorylation	0.0259099367043505
GO:0010149	senescence	0.0259099367043505
GO:0008203	cholesterol metabolic process	0.030957613977377
GO:0042157	lipoprotein metabolic process	0.0319799892743909
GO:0051496	positive regulation of stress fiber formation	0.0319799892743909
GO:0051004	regulation of lipoprotein lipase activity	0.0319799892743909
GO:0051495	positive regulation of cytoskeleton organization and biogenesis	0.0319799892743909
GO:0032233	positive regulation of actin filament bundle formation	0.0319799892743909
GO:0031232	extrinsic to external side of plasma membrane	0.0319799892743909
GO:0043086	negative regulation of catalytic activity	0.0319799892743909
GO:0016125	sterol metabolic process	0.0363570142838911
GO:0005319	lipid transporter activity	0.0370265024419312
GO:0051721	protein phosphatase 2A binding	0.0374547283925113
GO:0045192	low-density lipoprotein catabolic process	0.0374547283925113
GO:0032088	inhibition of NF-kappaB transcription factor	0.0374547283925113
GO:0031589	cell-substrate adhesion	0.0389496332072172
GO:0035303	regulation of dephosphorylation	0.0439905280809569
GO:0017166	vinculin binding	0.0439905280809569
GO:0031324	negative regulation of cellular metabolic process	0.0444126921707153
GO:0051346	negative regulation of hydrolase activity	0.0454880282252511
GO:0006423	cysteinyl-tRNA aminoacylation	0.0454880282252511
GO:0004817	cysteine-tRNA ligase activity	0.0454880282252511
GO:0033344	cholesterol efflux	0.0454880282252511
GO:0042159	lipoprotein catabolic process	0.0454880282252511
GO:0051492	regulation of stress fiber formation	0.0454880282252511
GO:0032231	regulation of actin filament bundle formation	0.0454880282252511
GO:0043038	amino acid activation	0.0456459809016163
GO:0006418	tRNA aminoacylation for protein translation	0.0456459809016163
GO:0043039	tRNA aminoacylation	0.0456459809016163
GO:0001953	negative regulation of cell-matrix adhesion	0.0456459809016163
GO:0043149	stress fiber formation	0.0456459809016163
GO:0006869	lipid transport	0.0456459809016163
GO:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	0.0456459809016163
GO:0016875	ligase activity, forming carbon-oxygen bonds	0.0456459809016163
GO:0004812	aminoacyl-tRNA ligase activity	0.0456459809016163
GO:0006915	apoptosis	0.0456459809016163
GO:0009892	negative regulation of metabolic process	0.0456459809016163
GO:0012501	programmed cell death	0.0456459809016163
GO:0030299	cholesterol absorption	0.0456459809016163
GO:0043410	positive regulation of MAPKKK cascade	0.0456459809016163
GO:0000045	autophagic vacuole formation	0.0456459809016163
GO:0042627	chylomicron	0.0456459809016163
GO:0044241	lipid digestion	0.0456459809016163
GO:0050750	low-density lipoprotein receptor binding	0.0456459809016163
GO:0045471	response to ethanol	0.0456459809016163
GO:0000267	cell fraction	0.0469230363482118
GO:0045736	negative regulation of cyclin-dependent protein kinase activity	0.0469230363482118
GO:0016236	macroautophagy	0.0469230363482118
GO:0006707	cholesterol catabolic process	0.0469230363482118
GO:0016127	sterol catabolic process	0.0469230363482118
GO:0048168	regulation of neuronal synaptic plasticity	0.0469230363482118
GO:0016265	death	0.0469230363482118
GO:0008219	cell death	0.0469230363482118
GO:0050892	intestinal absorption	0.0498827202411778
GO:0001540	beta-amyloid binding	0.0498827202411778
GO:0022408	negative regulation of cell-cell adhesion	0.0498827202411778

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
fibroblast	1.04e-14	76
contractile cell	3.43e-14	59
muscle precursor cell	4.28e-14	58
myoblast	4.28e-14	58
multi-potent skeletal muscle stem cell	4.28e-14	58
muscle cell	8.18e-13	55
electrically responsive cell	6.87e-11	61
electrically active cell	6.87e-11	61
non-terminally differentiated cell	1.04e-10	106
cell of skeletal muscle	1.22e-09	9
somatic cell	8.33e-09	588
multi fate stem cell	3.67e-08	427
somatic stem cell	8.81e-08	433
stem cell	2.70e-07	441
skin fibroblast	4.89e-07	23
smooth muscle cell	5.91e-07	43
smooth muscle myoblast	5.91e-07	43

Uber Anatomy

Ontology term	p-value	n
muscle tissue	3.91e-13	64
musculature	3.91e-13	64
musculature of body	3.91e-13	64
skeletal muscle tissue	1.05e-12	62
striated muscle tissue	1.05e-12	62
myotome	1.05e-12	62
somite	3.50e-12	71
presomitic mesoderm	3.50e-12	71
presumptive segmental plate	3.50e-12	71
dermomyotome	3.50e-12	71
trunk paraxial mesoderm	3.50e-12	71
paraxial mesoderm	6.62e-12	72
presumptive paraxial mesoderm	6.62e-12	72
dense mesenchyme tissue	1.23e-11	73
articulation	1.67e-11	8
skeletal joint	1.67e-11	8
articular system	1.67e-11	8
multilaminar epithelium	2.92e-11	83
epithelial vesicle	2.10e-10	78
intervertebral cartilage	3.23e-10	5
symphysis	3.23e-10	5
nonsynovial joint	3.23e-10	5
fibrous joint	3.23e-10	5
cartilaginous joint	3.23e-10	5
developing mesenchymal condensation	3.23e-10	5
pre-cartilage condensation	3.23e-10	5
cartilaginous condensation	3.23e-10	5
cartilage element	3.23e-10	5
post-cranial axial skeletal system	3.23e-10	5
vertebral column	3.23e-10	5
intervertebral disk	3.23e-10	5
intervertebral joint	3.23e-10	5
mesenchyme	3.43e-08	160
entire embryonic mesenchyme	3.43e-08	160
trunk mesenchyme	2.13e-07	122
vasculature of eye	6.44e-07	6
uvea	6.44e-07	6
vasculature of head	6.44e-07	6
surface structure	9.12e-07	99

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
HNF4G#3174	8	2.64399287599511	0.0109263525724861	0.0402134593620846
NR3C1#2908	12	2.06524459740318	0.0128841073377866	0.0463441806871393

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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