Coexpression cluster:C1060

Full id: C1060_Mesenchymal_Pericytes_Fibroblast_occipital_Renal_temporal_Nucleus

Phase1 CAGE Peaks

Hg19::chr19:1885483..1885507,-	p1@FAM108A1
Hg19::chr19:2015699..2015748,-	p1@BTBD2
Hg19::chr19:40854559..40854625,+	p2@PLD3
Hg19::chr19:50270219..50270319,+	p1@AP2A1
Hg19::chr19:7580944..7581031,+	p1@ZNF358
Hg19::chr1:201857992..201858055,+	p1@SHISA4
Hg19::chr4:102268904..102268948,+	p1@FLJ20021
Hg19::chrX:48455870..48455905,+	p1@WDR13

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:0030128	clathrin coat of endocytic vesicle	0.022949948668774
GO:0030669	clathrin-coated endocytic vesicle membrane	0.022949948668774
GO:0030122	AP-2 adaptor complex	0.022949948668774
GO:0030666	endocytic vesicle membrane	0.022949948668774
GO:0004630	phospholipase D activity	0.022949948668774
GO:0006895	Golgi to endosome transport	0.022949948668774
GO:0045334	clathrin-coated endocytic vesicle	0.022949948668774
GO:0030132	clathrin coat of coated pit	0.0372772031699452
GO:0030130	clathrin coat of trans-Golgi network vesicle	0.0376591196280217
GO:0012510	trans-Golgi network transport vesicle membrane	0.0376591196280217
GO:0006892	post-Golgi vesicle-mediated transport	0.0376591196280217
GO:0030125	clathrin vesicle coat	0.0376591196280217
GO:0030139	endocytic vesicle	0.0376591196280217
GO:0030665	clathrin coated vesicle membrane	0.0376591196280217
GO:0030140	trans-Golgi network transport vesicle	0.0431205011761095
GO:0030658	transport vesicle membrane	0.0431205011761095
GO:0030660	Golgi-associated vesicle membrane	0.0431205011761095

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
non-terminally differentiated cell	4.19e-17	180
mesodermal cell	2.45e-14	119
contractile cell	5.42e-14	59
muscle cell	7.29e-12	54
muscle precursor cell	7.41e-12	57
myoblast	7.41e-12	57
multi-potent skeletal muscle stem cell	7.41e-12	57
electrically responsive cell	2.62e-10	60
electrically active cell	2.62e-10	60
smooth muscle cell	2.75e-10	42
smooth muscle myoblast	2.75e-10	42
embryonic cell	5.29e-09	248
vascular associated smooth muscle cell	5.02e-08	32

Uber Anatomy

Ontology term	p-value	n
epithelium	1.33e-28	309
organism subdivision	1.75e-28	365
cell layer	2.67e-28	312
multi-cellular organism	7.34e-24	659
anatomical conduit	2.50e-23	241
tube	5.29e-23	194
anatomical cluster	1.74e-22	286
multi-tissue structure	3.41e-22	347
anatomical system	1.33e-19	625
anatomical group	2.74e-19	626
embryonic structure	1.19e-17	605
developing anatomical structure	1.19e-17	605
germ layer	1.61e-17	604
embryonic tissue	1.61e-17	604
presumptive structure	1.61e-17	604
epiblast (generic)	1.61e-17	604
embryo	2.43e-17	612
neural plate	2.76e-17	86
presumptive neural plate	2.76e-17	86
neurectoderm	3.05e-16	90
head	3.96e-16	123
regional part of brain	4.49e-16	59
ectoderm-derived structure	7.47e-16	169
neural tube	1.00e-15	57
neural rod	1.00e-15	57
future spinal cord	1.00e-15	57
neural keel	1.00e-15	57
brain	1.57e-15	69
future brain	1.57e-15	69
ectoderm	2.73e-15	173
presumptive ectoderm	2.73e-15	173
adult organism	8.98e-15	115
anterior region of body	2.83e-14	129
craniocervical region	2.83e-14	129
pre-chordal neural plate	2.95e-14	61
organ part	3.32e-14	219
central nervous system	4.29e-14	82
somite	4.81e-14	83
paraxial mesoderm	4.81e-14	83
presomitic mesoderm	4.81e-14	83
presumptive segmental plate	4.81e-14	83
trunk paraxial mesoderm	4.81e-14	83
presumptive paraxial mesoderm	4.81e-14	83
multilaminar epithelium	9.53e-14	82
trunk mesenchyme	1.39e-13	143
dermomyotome	1.89e-13	70
vasculature	3.66e-13	79
vascular system	3.66e-13	79
regional part of nervous system	3.82e-13	94
nervous system	3.82e-13	94
splanchnic layer of lateral plate mesoderm	4.67e-13	84
skeletal muscle tissue	8.23e-13	61
striated muscle tissue	8.23e-13	61
myotome	8.23e-13	61
circulatory system	8.71e-13	113
muscle tissue	1.41e-12	63
musculature	1.41e-12	63
musculature of body	1.41e-12	63
anterior neural tube	1.43e-12	42
regional part of forebrain	1.51e-12	41
forebrain	1.51e-12	41
future forebrain	1.51e-12	41
telencephalon	3.40e-12	34
epithelial tube	4.93e-12	118
cerebral hemisphere	5.06e-12	32
cardiovascular system	5.13e-12	110
gray matter	9.69e-12	34
brain grey matter	9.69e-12	34
regional part of telencephalon	1.20e-11	33
vessel	5.16e-11	69
trunk	5.19e-11	216
regional part of cerebral cortex	1.24e-10	22
blood vessel	1.57e-10	60
epithelial tube open at both ends	1.57e-10	60
blood vasculature	1.57e-10	60
vascular cord	1.57e-10	60
cerebral cortex	8.37e-10	25
pallium	8.37e-10	25
neocortex	9.86e-10	20
unilaminar epithelium	2.59e-09	138
artery	1.95e-08	42
arterial blood vessel	1.95e-08	42
arterial system	1.95e-08	42
compound organ	1.07e-07	69

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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No analysis results for this cluster

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.