Coexpression cluster:C1158

Full id: C1158_Small_malignant_Gingival_Keratinocyte_cervical_Mallassezderived_oral

Phase1 CAGE Peaks

Hg19::chr11:94439579..94439590,+	p11@AMOTL1
Hg19::chr11:94439591..94439602,+	p7@AMOTL1
Hg19::chr11:94439606..94439641,+	p2@AMOTL1
Hg19::chr11:94439650..94439668,+	p4@AMOTL1
Hg19::chr11:94439679..94439690,+	p9@AMOTL1
Hg19::chr14:81790540..81790556,-	p@chr14:81790540..81790556 -
Hg19::chr1:209605563..209605577,+	p1@MIR205 p2@MIR205HG

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:0005923	tight junction	0.0123631225715295
GO:0043296	apical junction complex	0.0123631225715295
GO:0016327	apicolateral plasma membrane	0.0123631225715295
GO:0005911	intercellular junction	0.0152772871776757
GO:0042802	identical protein binding	0.0252560932532674
GO:0030054	cell junction	0.0252560932532674

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
endo-epithelial cell	1.44e-18	42
general ecto-epithelial cell	8.86e-14	14
endodermal cell	1.04e-13	58
epithelial cell of alimentary canal	7.04e-13	20
epithelial cell	3.46e-11	253
respiratory epithelial cell	1.16e-09	13
acinar cell	1.22e-09	5
protein secreting cell	6.52e-08	6
transitional epithelial cell	2.40e-07	4
urothelial cell	2.40e-07	4
stratified squamous epithelial cell	3.27e-07	6
keratin accumulating cell	3.27e-07	6
stratified epithelial cell	3.27e-07	6
keratinizing barrier epithelial cell	3.27e-07	6
epithelial fate stem cell	3.27e-07	6
stratified epithelial stem cell	3.27e-07	6
surface ectodermal cell	3.27e-07	6
gingival epithelial cell	7.50e-07	3
squamous epithelial cell	8.85e-07	63
ecto-epithelial cell	9.24e-07	34

Uber Anatomy

Ontology term	p-value	n
oral opening	5.74e-13	22
orifice	8.02e-13	36
respiratory system	2.20e-12	74
mouth	2.05e-10	29
stomodeum	2.05e-10	29
surface structure	5.21e-10	99
anterior region of body	7.44e-10	62
craniocervical region	7.44e-10	62
endoderm-derived structure	3.29e-09	160
endoderm	3.29e-09	160
presumptive endoderm	3.29e-09	160
urothelium	8.26e-09	5
ectoderm-derived structure	1.15e-07	171
ectoderm	1.15e-07	171
presumptive ectoderm	1.15e-07	171
neck	1.16e-07	10
head	1.39e-07	56
gland of gut	2.01e-07	10
transitional epithelium	3.10e-07	6
saliva-secreting gland	3.14e-07	6
gland of oral region	3.14e-07	6
gland of foregut	3.14e-07	6
oral gland	3.14e-07	6
oral cavity	3.14e-07	6
respiratory tract	5.16e-07	54
gingival epithelium	7.50e-07	3

Disease

Ontology term	p-value	n
squamous cell carcinoma	1.25e-13	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
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223300339091182
STAT3#6774	5	7.51390356939589	0.000138182044941322	0.0018050774973892
TRIM28#10155	5	13.2789464609018	8.62103642667186e-06	0.000234045340100125

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.