Coexpression cluster:C544

Full id: C544_nasal_Keratinocyte_Esophageal_Urothelial_Placental_Corneal_Prostate

Phase1 CAGE Peaks

Hg19::chr17:39775781..39775811,-	p@chr17:39775781..39775811 -
Hg19::chr17:39775857..39775872,-	p@chr17:39775857..39775872 -
Hg19::chr17:39776987..39777014,-	p@chr17:39776987..39777014 -
Hg19::chr17:39777017..39777027,+	p@chr17:39777017..39777027 +
Hg19::chr17:39777054..39777079,-	p5@KRT17
Hg19::chr17:39777082..39777104,-	p6@KRT17
Hg19::chr17:39777267..39777358,-	p1@EF608070
Hg19::chr17:39777878..39777913,+	p@chr17:39777878..39777913 +
Hg19::chr17:39777922..39777964,-	p@chr17:39777922..39777964 -
Hg19::chr17:39777995..39778013,-	p@chr17:39777995..39778013 -
Hg19::chr17:39779227..39779270,-	p3@KRT17
Hg19::chr17:39780328..39780347,+	p@chr17:39780328..39780347 +
Hg19::chr17:39780497..39780517,+	p@chr17:39780497..39780517 +
Hg19::chr17:39780530..39780549,-	p2@KRT17
Hg19::chr17:39780624..39780631,-	p8@KRT17
Hg19::chr17:39780634..39780644,-	p4@KRT17
Hg19::chr17:39780819..39780835,-	p1@KRT17

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

---

GO ID	GO name	FDR corrected p-value
GO:0005200	structural constituent of cytoskeleton	0.0347344872247733
GO:0008544	epidermis development	0.0347344872247733
GO:0007398	ectoderm development	0.0347344872247733
GO:0045111	intermediate filament cytoskeleton	0.0347344872247733
GO:0005882	intermediate filament	0.0347344872247733
GO:0009888	tissue development	0.0374082577809176

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	8.00e-16	254
endo-epithelial cell	2.38e-14	43
endodermal cell	1.21e-09	59
respiratory epithelial cell	2.72e-09	13
general ecto-epithelial cell	5.20e-07	13

Uber Anatomy

Ontology term	p-value	n
organ	2.49e-14	511
respiratory system	1.13e-13	72
organ part	2.96e-12	219
respiratory tract	4.04e-11	53
endoderm-derived structure	4.23e-10	169
endoderm	4.23e-10	169
presumptive endoderm	4.23e-10	169
embryo	2.18e-09	612
embryonic structure	5.70e-09	605
developing anatomical structure	5.70e-09	605
germ layer	1.00e-08	604
embryonic tissue	1.00e-08	604
presumptive structure	1.00e-08	604
epiblast (generic)	1.00e-08	604
anatomical group	1.05e-08	626
anatomical system	1.40e-08	625
extraembryonic membrane	3.09e-08	14
membranous layer	3.09e-08	14
upper respiratory tract	5.20e-08	19
multi-cellular organism	5.35e-08	659
segment of respiratory tract	5.97e-08	46
larynx	1.12e-07	9
ectoderm	1.84e-07	173
presumptive ectoderm	1.84e-07	173
mixed endoderm/mesoderm-derived structure	1.94e-07	130
ectoderm-derived structure	2.20e-07	169
orifice	2.38e-07	35
anterior region of body	2.41e-07	129
craniocervical region	2.41e-07	129
respiratory primordium	2.73e-07	38
endoderm of foregut	2.73e-07	38
oral opening	7.65e-07	21

Disease

Ontology term	p-value	n
squamous cell carcinoma	3.62e-08	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
CTCF#10664	8	2.52247358732942	0.00710763553513563	0.0296309415477419
GATA2#2624	5	3.74850933339823	0.00825039453437635	0.0325131293779991
STAT3#6774	6	3.71275235193679	0.00361806375137964	0.0183119437911479

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.