Coexpression cluster:C3242

Full id: C3242_Small_Tracheal_Bronchial_Mallassezderived_Keratinocyte_Gingival_Mammary

Phase1 CAGE Peaks

Hg19::chr12:116955659..116955671,+	p1@ENST00000552992
Hg19::chr12:28187330..28187352,-	p@chr12:28187330..28187352 -
Hg19::chr14:85799279..85799283,+	p@chr14:85799279..85799283 +

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

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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

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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>

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Cell Type

Ontology term	p-value	n
general ecto-epithelial cell	2.45e-28	13
endo-epithelial cell	2.33e-27	43
respiratory epithelial cell	1.82e-23	13
epithelial cell	7.61e-19	254
endodermal cell	2.16e-18	59
squamous epithelial cell	9.17e-15	62
epidermal cell	3.14e-14	8
stratified squamous epithelial cell	1.21e-13	6
keratin accumulating cell	1.21e-13	6
stratified epithelial cell	1.21e-13	6
keratinizing barrier epithelial cell	1.21e-13	6
epithelial fate stem cell	1.21e-13	6
stratified epithelial stem cell	1.21e-13	6
surface ectodermal cell	1.21e-13	6
ecto-epithelial cell	2.50e-13	33
epithelial cell of tracheobronchial tree	4.35e-13	9
epithelial cell of lower respiratory tract	4.35e-13	9
bronchial epithelial cell	4.79e-11	3
epithelial cell of Malassez	8.58e-11	3
keratinocyte	9.06e-11	5
duct epithelial cell	1.01e-10	3
branched duct epithelial cell	1.01e-10	3
tracheal epithelial cell	1.01e-10	3
tracheoblast	1.01e-10	3
gingival epithelial cell	1.22e-10	3
epithelial cell of alimentary canal	1.39e-10	21
mammary gland epithelial cell	1.30e-07	4
sebum secreting cell	1.82e-07	2
epithelial cell of sweat gland	1.82e-07	2
epithelial cell of skin gland	1.82e-07	2
acinar cell of sebaceous gland	1.82e-07	2
corneal epithelial cell	2.34e-07	2
embryonic cell	9.47e-07	248

Uber Anatomy

Ontology term	p-value	n
respiratory system	1.81e-15	72
surface structure	8.47e-14	95
orifice	1.22e-11	35
respiratory tract	2.87e-11	53
lower respiratory tract epithelium	4.79e-11	3
epithelium of bronchus	4.79e-11	3
gingival epithelium	1.22e-10	3
skin epidermis	2.26e-10	14
outer epithelium	2.26e-10	14
enveloping layer of ectoderm	2.26e-10	14
oral opening	2.33e-10	21
mouth mucosa	3.17e-10	5
endoderm-derived structure	1.37e-09	169
endoderm	1.37e-09	169
presumptive endoderm	1.37e-09	169
mouth	3.49e-09	28
stomodeum	3.49e-09	28
mucosa	1.76e-08	12
bronchus	2.30e-08	4
jaw skeleton	3.53e-08	4
tracheobronchial tree	4.05e-08	14
lower respiratory tract	4.05e-08	14
respiratory system epithelium	1.07e-07	28
mammary gland	1.30e-07	4
mammary bud	1.30e-07	4
mammary ridge	1.30e-07	4
mammary placode	1.30e-07	4
skin gland	1.82e-07	2
epidermis gland	1.82e-07	2
gland of integumental system	1.82e-07	2
sebaceous gland	1.82e-07	2
skin sebaceous gland	1.82e-07	2
sweat gland	1.82e-07	2
sweat gland placode	1.82e-07	2
sebaceous gland placode	1.82e-07	2
mucosa of oral region	1.95e-07	4
respiratory system mucosa	1.95e-07	4
neck	2.06e-07	10
segment of respiratory tract	3.01e-07	46
chordate pharynx	3.06e-07	10
pharyngeal region of foregut	3.06e-07	10
subdivision of head	9.16e-07	48

Disease

Ontology term	p-value	n
squamous cell carcinoma	1.69e-23	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

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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

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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

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This analysis result is provided for C0 - C305 clusters.