Coexpression cluster:C3301

Full id: C3301_Renal_Placental_Mesenchymal_Pericytes_Osteoblast_Astrocyte_Nucleus

Phase1 CAGE Peaks

Hg19::chr12:56546363..56546397,+	p1@MYL6B
Hg19::chr19:50354393..50354422,+	p1@PTOV1
Hg19::chr19:50354430..50354447,+	p2@PTOV1

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:0030049	muscle filament sliding	0.0107137600063315
GO:0033275	actin-myosin filament sliding	0.0107137600063315
GO:0016461	unconventional myosin complex	0.0107137600063315
GO:0030048	actin filament-based movement	0.0183640125820119
GO:0005859	muscle myosin complex	0.0198914181804517
GO:0016460	myosin II complex	0.0198914181804517
GO:0008307	structural constituent of muscle	0.0275354752527976
GO:0044449	contractile fiber part	0.0307366264913492
GO:0043292	contractile fiber	0.0307366264913492
GO:0007519	skeletal muscle development	0.0307366264913492
GO:0014706	striated muscle development	0.03668909487398
GO:0016459	myosin complex	0.0408816032450061

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
embryonic cell	2.41e-20	248
non-terminally differentiated cell	1.76e-19	180
mesodermal cell	1.07e-17	119
electrically responsive cell	4.73e-17	60
electrically active cell	4.73e-17	60
contractile cell	9.73e-17	59
muscle cell	3.16e-14	54
muscle precursor cell	1.82e-13	57
myoblast	1.82e-13	57
multi-potent skeletal muscle stem cell	1.82e-13	57
smooth muscle cell	1.66e-12	42
smooth muscle myoblast	1.66e-12	42
vascular associated smooth muscle cell	1.81e-10	32
neurectodermal cell	4.24e-10	59
ectodermal cell	1.22e-08	71
migratory neural crest cell	1.87e-07	41
meso-epithelial cell	2.76e-07	44
endothelial cell	5.94e-07	35

Uber Anatomy

Ontology term	p-value	n
cell layer	2.97e-31	312
epithelium	9.54e-31	309
multi-tissue structure	4.57e-23	347
anatomical cluster	9.11e-23	286
tube	3.07e-21	194
organism subdivision	7.11e-21	365
anatomical conduit	5.75e-19	241
vasculature	3.12e-16	79
vascular system	3.12e-16	79
epithelial tube	1.57e-15	118
trunk mesenchyme	1.60e-15	143
dermomyotome	1.68e-15	70
somite	3.13e-15	83
paraxial mesoderm	3.13e-15	83
presomitic mesoderm	3.13e-15	83
presumptive segmental plate	3.13e-15	83
trunk paraxial mesoderm	3.13e-15	83
presumptive paraxial mesoderm	3.13e-15	83
multilaminar epithelium	7.43e-15	82
ectoderm	2.59e-14	173
presumptive ectoderm	2.59e-14	173
splanchnic layer of lateral plate mesoderm	3.84e-14	84
skeletal muscle tissue	4.08e-14	61
striated muscle tissue	4.08e-14	61
myotome	4.08e-14	61
unilaminar epithelium	5.24e-14	138
ectoderm-derived structure	1.88e-13	169
neurectoderm	7.35e-13	90
muscle tissue	7.77e-13	63
musculature	7.77e-13	63
musculature of body	7.77e-13	63
regional part of nervous system	1.05e-12	94
nervous system	1.05e-12	94
embryo	1.14e-12	612
vessel	3.30e-12	69
blood vessel	3.56e-12	60
epithelial tube open at both ends	3.56e-12	60
blood vasculature	3.56e-12	60
vascular cord	3.56e-12	60
central nervous system	4.29e-12	82
organ part	4.76e-12	219
neural plate	5.92e-12	86
presumptive neural plate	5.92e-12	86
multi-cellular organism	7.25e-12	659
head	1.41e-11	123
pre-chordal neural plate	2.44e-11	61
artery	5.93e-11	42
arterial blood vessel	5.93e-11	42
arterial system	5.93e-11	42
anterior region of body	1.10e-10	129
craniocervical region	1.10e-10	129
embryonic structure	1.41e-10	605
developing anatomical structure	1.41e-10	605
germ layer	1.64e-10	604
embryonic tissue	1.64e-10	604
presumptive structure	1.64e-10	604
epiblast (generic)	1.64e-10	604
circulatory system	3.62e-10	113
cardiovascular system	3.69e-10	110
trunk	5.79e-10	216
brain	6.96e-10	69
future brain	6.96e-10	69
regional part of brain	2.45e-09	59
mesenchyme	4.75e-09	238
entire embryonic mesenchyme	4.75e-09	238
anatomical system	3.26e-08	625
neural tube	4.06e-08	57
neural rod	4.06e-08	57
future spinal cord	4.06e-08	57
neural keel	4.06e-08	57
anatomical group	4.61e-08	626
systemic artery	1.14e-07	33
systemic arterial system	1.14e-07	33
telencephalon	2.14e-07	34
compound organ	2.36e-07	69
gray matter	2.66e-07	34
brain grey matter	2.66e-07	34
cerebral hemisphere	3.20e-07	32
regional part of telencephalon	3.73e-07	33

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
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296119468782667
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189469517231388
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032412311509384
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320970565778059
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319491025432939
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167048420122484
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580023478750516
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108447989815185
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127756657130778
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156329187714242
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293558291698993
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172484844276618
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275770368985607
SIX5#147912	3	17.086715355459	0.000200406054632501	0.0023917504216391
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245726428336867
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374173239227808
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158625599166763
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189722329822594
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139777270247338

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.