Coexpression cluster:C2304

Full id: C2304_malignant_mesothelioma_Keratinocyte_Mesenchymal_oral_epidermoid_Mammary

Phase1 CAGE Peaks

Hg19::chr14:59830347..59830363,+	p@chr14:59830347..59830363 +
Hg19::chr14:59830369..59830387,+	p@chr14:59830369..59830387 +
Hg19::chr14:59830398..59830424,+	p@chr14:59830398..59830424 +
Hg19::chr14:59830427..59830451,+	p@chr14:59830427..59830451 +

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
epithelial cell	6.02e-20	254
squamous epithelial cell	1.03e-18	62
embryonic cell	3.57e-16	248
mesodermal cell	5.25e-11	119
endo-epithelial cell	4.62e-08	43
cardiocyte	4.72e-08	16
vascular associated smooth muscle cell	6.31e-07	32
endodermal cell	9.19e-07	59
muscle precursor cell	9.48e-07	57
myoblast	9.48e-07	57
multi-potent skeletal muscle stem cell	9.48e-07	57

Uber Anatomy

Ontology term	p-value	n
splanchnic layer of lateral plate mesoderm	2.14e-18	84
blood vessel	1.59e-12	60
epithelial tube open at both ends	1.59e-12	60
blood vasculature	1.59e-12	60
vascular cord	1.59e-12	60
unilaminar epithelium	3.86e-12	138
epithelial tube	4.25e-12	118
vasculature	6.83e-12	79
vascular system	6.83e-12	79
epithelium	1.48e-11	309
vessel	1.50e-11	69
primordium	1.56e-11	168
cell layer	2.12e-11	312
artery	8.65e-11	42
arterial blood vessel	8.65e-11	42
arterial system	8.65e-11	42
circulatory system	1.38e-10	113
cardiovascular system	3.01e-10	110
multilaminar epithelium	8.68e-10	82
anatomical cluster	1.45e-09	286
primary circulatory organ	1.65e-09	27
heart	2.23e-09	24
primitive heart tube	2.23e-09	24
primary heart field	2.23e-09	24
anterior lateral plate mesoderm	2.23e-09	24
heart tube	2.23e-09	24
heart primordium	2.23e-09	24
cardiac mesoderm	2.23e-09	24
cardiogenic plate	2.23e-09	24
heart rudiment	2.23e-09	24
systemic artery	4.33e-09	33
systemic arterial system	4.33e-09	33
anatomical conduit	6.93e-08	241
trunk	1.58e-07	216
multi-cellular organism	2.81e-07	659
skeletal muscle tissue	4.59e-07	61
striated muscle tissue	4.59e-07	61
myotome	4.59e-07	61
muscle tissue	4.82e-07	63
musculature	4.82e-07	63
musculature of body	4.82e-07	63
aorta	4.92e-07	21
aortic system	4.92e-07	21
mesenchyme	6.55e-07	238
entire embryonic mesenchyme	6.55e-07	238
multi-tissue structure	6.74e-07	347

Disease

Ontology term	p-value	n
squamous cell carcinoma	1.49e-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
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00267734218760267
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101333845633189
EP300#2033	4	6.7739417262232	0.000474845982144264	0.0043372782516324
ESR1#2099	4	30.7686032961545	1.11467714392546e-06	4.59596392555984e-05
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00194629645413906
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000720602239631222
NR3C1#2908	4	14.973023331173	1.98868032687801e-05	0.000442094049933615
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321627802875635
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243752876480969

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.