Coexpression cluster:C1811

Full id: C1811_Mesenchymal_Alveolar_Pericytes_Placental_Renal_Melanocyte_Fibroblast

Phase1 CAGE Peaks

Hg19::chr19:15236470..15236542,-	p1@ILVBL
Hg19::chr19:1905365..1905411,+	p1@ADAT3 p1@SCAMP4
Hg19::chr1:11986442..11986502,-	p1@KIAA2013
Hg19::chr3:50396911..50396972,-	p1@TMEM115
Hg19::chr3:51705222..51705281,+	p1@TEX264

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

---

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

---

No GOStat results

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	6.82e-20	121
embryonic cell	8.55e-19	250
contractile cell	3.86e-15	59
smooth muscle cell	1.04e-13	43
smooth muscle myoblast	1.04e-13	43
muscle precursor cell	1.82e-13	58
myoblast	1.82e-13	58
multi-potent skeletal muscle stem cell	1.82e-13	58
muscle cell	4.68e-13	55
somatic cell	1.68e-12	588
vascular associated smooth muscle cell	4.32e-11	32
non-terminally differentiated cell	5.35e-11	106
electrically responsive cell	4.31e-10	61
electrically active cell	4.31e-10	61
extraembryonic cell	3.33e-08	19
meso-epithelial cell	4.28e-08	45
endothelial cell	5.19e-08	36
fibroblast	1.12e-07	76
animal cell	1.22e-07	679
eukaryotic cell	1.22e-07	679
lining cell	2.48e-07	58
barrier cell	2.48e-07	58

Uber Anatomy

Ontology term	p-value	n
epithelial tube	1.54e-17	117
epithelial vesicle	9.66e-16	78
splanchnic layer of lateral plate mesoderm	1.13e-15	83
unilaminar epithelium	1.67e-14	148
vasculature	2.44e-14	78
vascular system	2.44e-14	78
cell layer	8.28e-14	309
mesenchyme	1.71e-13	160
entire embryonic mesenchyme	1.71e-13	160
epithelium	1.88e-13	306
vessel	5.79e-13	68
somite	5.82e-13	71
presomitic mesoderm	5.82e-13	71
presumptive segmental plate	5.82e-13	71
dermomyotome	5.82e-13	71
trunk paraxial mesoderm	5.82e-13	71
artery	6.05e-13	42
arterial blood vessel	6.05e-13	42
arterial system	6.05e-13	42
dense mesenchyme tissue	8.12e-13	73
multilaminar epithelium	1.00e-12	83
paraxial mesoderm	1.29e-12	72
presumptive paraxial mesoderm	1.29e-12	72
trunk mesenchyme	1.41e-12	122
epithelial tube open at both ends	6.89e-12	59
blood vessel	6.89e-12	59
blood vasculature	6.89e-12	59
vascular cord	6.89e-12	59
skeletal muscle tissue	1.20e-11	62
striated muscle tissue	1.20e-11	62
myotome	1.20e-11	62
circulatory system	1.35e-11	112
multi-cellular organism	1.39e-11	656
trunk	2.29e-11	199
cardiovascular system	3.14e-11	109
muscle tissue	3.33e-11	64
musculature	3.33e-11	64
musculature of body	3.33e-11	64
organism subdivision	4.03e-11	264
anatomical group	1.07e-09	625
multi-tissue structure	1.20e-09	342
anatomical system	1.33e-09	624
systemic artery	1.67e-09	33
systemic arterial system	1.67e-09	33
anatomical conduit	1.37e-08	240
anatomical cluster	2.11e-08	373
mesoderm	8.81e-08	315
mesoderm-derived structure	8.81e-08	315
presumptive mesoderm	8.81e-08	315
developing anatomical structure	3.40e-07	581
tube	3.65e-07	192
parenchyma	8.16e-07	15
extraembryonic membrane	9.31e-07	14
membranous layer	9.31e-07	14

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	4	17.970539620807	1.89252338486495e-05	0.000428935003888694
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00573188015040229
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00674348975015004
IRF1#3659	5	7.6371637535639	3.84754333311872e-05	0.000724285468939413
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329532955674077
MYC#4609	4	4.17782549728752	0.00569196903682344	0.0256809899013653
NRF1#4899	4	9.76822355816873	0.000210129774810679	0.00244520819514791
PAX5#5079	4	5.33565242494226	0.00222338958618779	0.0127790757246088
SIX5#147912	3	10.2520292132754	0.00183229106867769	0.0108494527112841
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204300467499354
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135381171921401
YY1#7528	4	3.92893659988308	0.00719386626991762	0.029843900669868

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.