Coexpression cluster:C1142

Full id: C1142_Mesenchymal_Fibroblast_Pericytes_Smooth_Renal_Hepatic_Hair

Phase1 CAGE Peaks

Hg19::chr11:46958264..46958342,+	p1@C11orf49
Hg19::chr20:327736..327767,+	p1@NRSN2
Hg19::chr2:27545939..27545981,-	p1@MPV17
Hg19::chrX:134156502..134156577,-	p1@FAM127C
Hg19::chrX:134166360..134166371,+	p2@FAM127A
Hg19::chrX:134166376..134166394,+	p1@FAM127A
Hg19::chrX:48931650..48931681,-	p1@PRAF2

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:0000002	mitochondrial genome maintenance	0.0240980092024216
GO:0015813	L-glutamate transport	0.0240980092024216
GO:0015800	acidic amino acid transport	0.0240980092024216
GO:0005779	integral to peroxisomal membrane	0.0240980092024216
GO:0031231	intrinsic to peroxisomal membrane	0.0240980092024216
GO:0043025	cell soma	0.0321322983860711
GO:0031903	microbody membrane	0.0321322983860711
GO:0006800	oxygen and reactive oxygen species metabolic process	0.0321322983860711
GO:0005778	peroxisomal membrane	0.0321322983860711
GO:0044439	peroxisomal part	0.0321322983860711
GO:0044438	microbody part	0.0321322983860711
GO:0016020	membrane	0.036124967424513
GO:0030133	transport vesicle	0.0364189068602428
GO:0006865	amino acid transport	0.0375136993092468
GO:0015837	amine transport	0.0375136993092468
GO:0007005	mitochondrion organization and biogenesis	0.0375136993092468
GO:0046942	carboxylic acid transport	0.0375136993092468
GO:0015849	organic acid transport	0.0375136993092468
GO:0042579	microbody	0.0375136993092468
GO:0005777	peroxisome	0.0375136993092468
GO:0031301	integral to organelle membrane	0.0495754959062544

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
contractile cell	3.97e-19	59
non-terminally differentiated cell	9.71e-19	106
muscle precursor cell	5.07e-17	58
myoblast	5.07e-17	58
multi-potent skeletal muscle stem cell	5.07e-17	58
muscle cell	1.03e-16	55
mesodermal cell	1.67e-16	121
smooth muscle cell	2.87e-15	43
smooth muscle myoblast	2.87e-15	43
electrically responsive cell	6.60e-15	61
electrically active cell	6.60e-15	61
fibroblast	8.11e-14	76
embryonic cell	1.27e-13	250
vascular associated smooth muscle cell	5.70e-11	32

Uber Anatomy

Ontology term	p-value	n
cell layer	1.28e-32	309
epithelium	2.76e-31	306
multi-tissue structure	9.22e-27	342
anatomical cluster	9.11e-26	373
multi-cellular organism	2.99e-23	656
tube	1.41e-20	192
structure with developmental contribution from neural crest	4.32e-20	132
anatomical system	1.25e-19	624
epithelial vesicle	1.30e-19	78
anatomical conduit	2.34e-19	240
anatomical group	3.12e-19	625
dense mesenchyme tissue	8.97e-18	73
paraxial mesoderm	1.95e-17	72
presumptive paraxial mesoderm	1.95e-17	72
somite	5.26e-17	71
presomitic mesoderm	5.26e-17	71
presumptive segmental plate	5.26e-17	71
dermomyotome	5.26e-17	71
trunk paraxial mesoderm	5.26e-17	71
ectoderm-derived structure	8.00e-17	171
ectoderm	8.00e-17	171
presumptive ectoderm	8.00e-17	171
multilaminar epithelium	3.14e-16	83
mesenchyme	3.56e-16	160
entire embryonic mesenchyme	3.56e-16	160
neural plate	4.84e-16	82
presumptive neural plate	4.84e-16	82
developing anatomical structure	5.22e-16	581
embryo	9.85e-16	592
ecto-epithelium	1.29e-15	104
skeletal muscle tissue	2.10e-15	62
striated muscle tissue	2.10e-15	62
myotome	2.10e-15	62
brain	4.01e-15	68
future brain	4.01e-15	68
central nervous system	5.66e-15	81
neurectoderm	7.11e-15	86
muscle tissue	1.38e-14	64
musculature	1.38e-14	64
musculature of body	1.38e-14	64
embryonic structure	4.31e-14	564
organ part	5.33e-14	218
germ layer	6.09e-14	560
germ layer / neural crest	6.09e-14	560
embryonic tissue	6.09e-14	560
presumptive structure	6.09e-14	560
germ layer / neural crest derived structure	6.09e-14	560
epiblast (generic)	6.09e-14	560
nervous system	1.17e-13	89
neural tube	1.99e-13	56
neural rod	1.99e-13	56
future spinal cord	1.99e-13	56
neural keel	1.99e-13	56
regional part of nervous system	2.74e-13	53
regional part of brain	2.74e-13	53
organism subdivision	3.23e-13	264
pre-chordal neural plate	3.76e-13	61
trunk mesenchyme	6.03e-13	122
vasculature	3.86e-12	78
vascular system	3.86e-12	78
splanchnic layer of lateral plate mesoderm	2.28e-11	83
epithelial tube	3.80e-11	117
unilaminar epithelium	4.28e-11	148
trunk	6.57e-11	199
regional part of forebrain	2.02e-10	41
forebrain	2.02e-10	41
anterior neural tube	2.02e-10	41
future forebrain	2.02e-10	41
telencephalon	6.84e-10	34
cerebral hemisphere	1.76e-09	32
epithelial tube open at both ends	2.27e-09	59
blood vessel	2.27e-09	59
blood vasculature	2.27e-09	59
vascular cord	2.27e-09	59
artery	2.47e-09	42
arterial blood vessel	2.47e-09	42
arterial system	2.47e-09	42
brain grey matter	2.61e-09	34
gray matter	2.61e-09	34
regional part of telencephalon	5.03e-09	32
vessel	5.10e-09	68
organ system subdivision	5.10e-08	223
regional part of cerebral cortex	8.41e-08	22
cerebral cortex	8.81e-08	25
pallium	8.81e-08	25
cardiovascular system	1.16e-07	109

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
E2F6#1876	5	3.58368266549813	0.00459810189782724	0.0217235666383416
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.0365591501783048
ELK4#2005	3	6.95814928220058	0.00677358459060016	0.0287513270090506
ETS1#2113	4	5.55929195554419	0.00302256447530346	0.0160484804898942
GABPB1#2553	5	5.04834559727298	0.000926743835001804	0.00673637245154186
HEY1#23462	5	2.88579360221836	0.0123136694185303	0.0446211901183818
MYC#4609	5	3.73020133686386	0.00382194422230669	0.0188683541779006
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223260121100441
SIX5#147912	3	7.32287800948243	0.0058666762526916	0.0263304598691387
SREBF1#6720	2	13.4302426972824	0.00884947602167745	0.0335900572861338
TAF1#6872	6	2.86546824492454	0.00372833020747146	0.0185836433225844
USF1#7391	5	4.54392805514854	0.00152278835596876	0.00970279379592589
YY1#7528	5	3.50797910703847	0.00507257067280898	0.0236116329499264
ZNF143#7702	3	5.78608995095481	0.011330055887324	0.0415513626945795

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.