Coexpression cluster:C4680

Full id: C4680_Smooth_clear_gastric_Mesothelial_glioma_rectum_melanoma

Phase1 CAGE Peaks

Hg19::chr7:27183263..27183284,-	p2@HOXA5
Hg19::chr7:27183291..27183324,-	p1@HOXA5
Hg19::chr7:27183325..27183338,-	p5@HOXA5

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	2.53e-12	119
kidney cell	1.52e-10	18
kidney epithelial cell	1.52e-10	18
epithelial cell of nephron	1.68e-09	16
endothelial cell of vascular tree	8.71e-09	24
lining cell	1.31e-08	57
barrier cell	1.31e-08	57
kidney tubule cell	4.12e-08	12
nephron tubule epithelial cell	4.12e-08	12
blood vessel endothelial cell	4.29e-08	18
embryonic blood vessel endothelial progenitor cell	4.29e-08	18
meso-epithelial cell	6.27e-08	44
kidney cortical cell	6.63e-08	13
renal cortical epithelial cell	6.63e-08	13
endothelial cell	9.37e-08	35
squamous epithelial cell	1.76e-07	62
preadipocyte	4.64e-07	12

Uber Anatomy

Ontology term	p-value	n
subdivision of trunk	2.09e-15	113
cavitated compound organ	5.79e-13	32
trunk	1.24e-12	216
epithelial tube	7.24e-12	118
renal system	8.65e-12	45
urinary system structure	1.75e-11	44
kidney	4.35e-11	27
kidney mesenchyme	4.35e-11	27
kidney rudiment	4.35e-11	27
kidney field	4.35e-11	27
intraembryonic coelom	7.43e-11	21
mesonephros	1.56e-10	18
pronephros	1.56e-10	18
nephrogenic cord	1.56e-10	18
pronephric mesoderm	1.56e-10	18
rostral part of nephrogenic cord	1.56e-10	18
presumptive pronephric mesoderm	1.56e-10	18
trunk region element	2.02e-10	107
abdominal segment of trunk	2.30e-10	61
abdomen	2.30e-10	61
excretory tube	3.60e-10	17
mesonephric epithelium	3.60e-10	17
mesonephric tubule	3.60e-10	17
nephric duct	3.60e-10	17
kidney epithelium	3.60e-10	17
renal duct	3.60e-10	17
mesonephric duct	3.60e-10	17
pronephric duct	3.60e-10	17
mesoderm	3.83e-10	448
mesoderm-derived structure	3.83e-10	448
presumptive mesoderm	3.83e-10	448
urogenital ridge	1.11e-09	20
nephron epithelium	1.68e-09	16
nephron	1.68e-09	16
uriniferous tubule	1.68e-09	16
metanephric mesenchyme	1.68e-09	16
nephrogenic mesenchyme	1.68e-09	16
vessel	4.73e-09	69
body cavity precursor	9.00e-09	63
blood vessel	9.63e-09	60
epithelial tube open at both ends	9.63e-09	60
blood vasculature	9.63e-09	60
vascular cord	9.63e-09	60
anatomical space	2.72e-08	104
compound organ	3.99e-08	69
renal tubule	4.12e-08	12
nephron tubule	4.12e-08	12
nephron tubule epithelium	4.12e-08	12
endothelium	4.29e-08	18
blood vessel endothelium	4.29e-08	18
cardiovascular system endothelium	4.29e-08	18
abdomen element	5.14e-08	55
abdominal segment element	5.14e-08	55
cortex of kidney	6.63e-08	13
renal parenchyma	6.63e-08	13
intermediate mesoderm	7.52e-08	37
immaterial anatomical entity	8.71e-08	126
simple squamous epithelium	8.74e-08	22
vasculature	4.93e-07	79
vascular system	4.93e-07	79
duct	7.05e-07	26
parenchyma	7.35e-07	17
squamous epithelium	7.54e-07	25

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.