Coexpression cluster:C566

Full id: C566_Pericytes_Renal_hepatic_Fibroblast_Endothelial_Hepatic_Lens

Phase1 CAGE Peaks

Hg19::chr13:110802350..110802403,-	p3@COL4A1
Hg19::chr13:110802503..110802522,-	p9@COL4A1
Hg19::chr13:110802740..110802769,-	p2@COL4A1
Hg19::chr13:110804802..110804837,-	p@chr13:110804802..110804837 -
Hg19::chr13:110829310..110829326,-	p@chr13:110829310..110829326 -
Hg19::chr13:110829341..110829354,-	p@chr13:110829341..110829354 -
Hg19::chr13:110839601..110839634,-	p@chr13:110839601..110839634 -
Hg19::chr13:110853822..110853836,-	p@chr13:110853822..110853836 -
Hg19::chr13:110861222..110861235,-	p@chr13:110861222..110861235 -
Hg19::chr13:110864247..110864268,-	p@chr13:110864247..110864268 -
Hg19::chr13:110959496..110959511,-	p1@COL4A1
Hg19::chr13:110959598..110959611,+	p2@COL4A2
Hg19::chr13:110959623..110959640,+	p1@COL4A2
Hg19::chr13:111009846..111009888,-	p@chr13:111009846..111009888 -
Hg19::chr13:111164370..111164403,+	p@chr13:111164370..111164403 +
Hg19::chr13:111164549..111164576,+	p@chr13:111164549..111164576 +

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

---

p.value	FDR	nGenes	nPathway	Name
4.88436109433595e-05	0.00386475071589332	2	200	Focal adhesion (KEGG):04510
8.76239653607e-06	0.00110931940146646	2	85	ECM-receptor interaction (KEGG):04512
7.95242710836606e-06	0.00110931940146646	2	81	Protein digestion and absorption (KEGG):04974
1.36590298944621e-05	0.00144102765386575	2	106	Amoebiasis (KEGG):05146
0.000130824789291056	0.00752837196556711	2	327	Pathways in cancer (KEGG):05200
8.76239653607e-06	0.00110931940146646	2	85	Small cell lung cancer (KEGG):05222
4.31443715156972e-05	0.00386475071589332	2	188	Focal Adhesion (Wikipathways):WP306
8.76239653607e-06	0.00110931940146646	2	85	Integrin cell surface interactions (Reactome):REACT_13552
5.10526184734612e-06	0.00110931940146646	2	65	Signaling by PDGF (Reactome):REACT_16888
8.58567593366187e-05	0.00603859207334218	2	265	Axon guidance (Reactome):REACT_18266
0.000816154648788236	0.0430521577235794	2	816	TGF beta receptor up reg. targets (Netpath):NetPath_7
0.000101437625782269	0.00642100171201764	2	288	{ACTB,297} (Static Module):NA

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

---

GO ID	GO name	FDR corrected p-value
GO:0005581	collagen	9.1276660944864e-05
GO:0005604	basement membrane	9.1276660944864e-05
GO:0005201	extracellular matrix structural constituent	0.00013724278986645
GO:0044420	extracellular matrix part	0.00013724278986645
GO:0006817	phosphate transport	0.00013724278986645
GO:0015698	inorganic anion transport	0.000379277449588247
GO:0006820	anion transport	0.000502106119333132
GO:0005578	proteinaceous extracellular matrix	0.000746924249734859
GO:0005587	collagen type IV	0.00127548516830642
GO:0030935	sheet-forming collagen	0.00137750370557821
GO:0044421	extracellular region part	0.00254125210080381
GO:0016525	negative regulation of angiogenesis	0.003251912687054
GO:0006811	ion transport	0.00483283573650064
GO:0045765	regulation of angiogenesis	0.0062286291620965
GO:0030198	extracellular matrix organization and biogenesis	0.00703642914021911
GO:0043062	extracellular structure organization and biogenesis	0.0120393189222703
GO:0001525	angiogenesis	0.0173898289872081
GO:0048514	blood vessel morphogenesis	0.0181053237656383
GO:0048646	anatomical structure formation	0.0181053237656383
GO:0001568	blood vessel development	0.0181053237656383
GO:0001944	vasculature development	0.0181053237656383
GO:0006810	transport	0.0250029879971245
GO:0051234	establishment of localization	0.0251161640147931
GO:0051179	localization	0.0282668149955082
GO:0009887	organ morphogenesis	0.0330695538606439

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>

---

Cell Type

Ontology term	p-value	n
mesodermal cell	2.61e-18	121
lining cell	1.50e-09	58
barrier cell	1.50e-09	58
contractile cell	3.72e-09	59
epithelial cell of nephron	1.53e-08	15
fibroblast	1.59e-08	76
endothelial cell	3.55e-08	36
muscle precursor cell	5.08e-08	58
myoblast	5.08e-08	58
multi-potent skeletal muscle stem cell	5.08e-08	58
meso-epithelial cell	5.65e-08	45
embryonic cell	1.67e-07	250
muscle cell	2.38e-07	55
smooth muscle cell	3.23e-07	43
smooth muscle myoblast	3.23e-07	43
kidney cortical cell	6.85e-07	12
renal cortical epithelial cell	6.85e-07	12
endothelial cell of vascular tree	7.48e-07	24
kidney cell	8.09e-07	17
kidney epithelial cell	8.09e-07	17

Uber Anatomy

Ontology term	p-value	n
vasculature	2.70e-17	78
vascular system	2.70e-17	78
epithelial tube	2.79e-16	117
circulatory system	9.65e-16	112
cardiovascular system	5.00e-15	109
splanchnic layer of lateral plate mesoderm	6.64e-14	83
vessel	1.00e-13	68
mesenchyme	6.40e-13	160
entire embryonic mesenchyme	6.40e-13	160
epithelial tube open at both ends	1.87e-10	59
blood vessel	1.87e-10	59
blood vasculature	1.87e-10	59
vascular cord	1.87e-10	59
trunk mesenchyme	8.10e-10	122
epithelial vesicle	1.45e-09	78
muscle tissue	1.46e-09	64
musculature	1.46e-09	64
musculature of body	1.46e-09	64
skeletal muscle tissue	3.46e-09	62
striated muscle tissue	3.46e-09	62
myotome	3.46e-09	62
trunk	3.86e-09	199
compound organ	4.44e-09	68
nephron epithelium	1.53e-08	15
renal tubule	1.53e-08	15
nephron tubule	1.53e-08	15
nephron	1.53e-08	15
uriniferous tubule	1.53e-08	15
nephrogenic mesenchyme	1.53e-08	15
excretory tube	1.60e-08	16
kidney epithelium	1.60e-08	16
parenchyma	5.55e-08	15
unilaminar epithelium	9.02e-08	148
organism subdivision	1.43e-07	264
mesoderm	3.75e-07	315
mesoderm-derived structure	3.75e-07	315
presumptive mesoderm	3.75e-07	315
artery	5.77e-07	42
arterial blood vessel	5.77e-07	42
arterial system	5.77e-07	42
dense mesenchyme tissue	6.75e-07	73
urogenital ridge	6.85e-07	11
cortex of kidney	6.85e-07	12
renal parenchyma	6.85e-07	12
somite	7.35e-07	71
presomitic mesoderm	7.35e-07	71
presumptive segmental plate	7.35e-07	71
dermomyotome	7.35e-07	71
trunk paraxial mesoderm	7.35e-07	71
abdominal segment of trunk	8.28e-07	60
abdomen	8.28e-07	60

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

---

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

---

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

---

This analysis result is provided for C0 - C305 clusters.