Coexpression cluster:C1109

Full id: C1109_Urothelial_Small_Gingival_Mallassezderived_Prostate_Sebocyte_Bronchial

Phase1 CAGE Peaks

Hg19::chr10:127763979..127763984,+	p@chr10:127763979..127763984 +
Hg19::chr12:28125953..28125964,-	p17@PTHLH
Hg19::chr12:28125967..28125978,-	p16@PTHLH
Hg19::chr1:116048147..116048169,+	p@chr1:116048147..116048169 +
Hg19::chr1:165873233..165873247,+	p6@UCK2
Hg19::chr6:151358048..151358060,+	p13@MTHFD1L
Hg19::chr8:141728760..141728771,-	p36@PTK2

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:0004849	uridine kinase activity	0.0336539626688756
GO:0004329	formate-tetrahydrofolate ligase activity	0.0336539626688756
GO:0019206	nucleoside kinase activity	0.0336539626688756
GO:0007172	signal complex assembly	0.0336539626688756
GO:0005524	ATP binding	0.0336539626688756
GO:0042169	SH2 domain binding	0.0336539626688756
GO:0032559	adenyl ribonucleotide binding	0.0336539626688756
GO:0030554	adenyl nucleotide binding	0.0336539626688756
GO:0007595	lactation	0.0336539626688756
GO:0046058	cAMP metabolic process	0.0336539626688756
GO:0005925	focal adhesion	0.0336539626688756
GO:0032553	ribonucleotide binding	0.0336539626688756
GO:0032555	purine ribonucleotide binding	0.0336539626688756
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0336539626688756
GO:0005924	cell-substrate adherens junction	0.0336539626688756
GO:0009396	folic acid and derivative biosynthetic process	0.0336539626688756
GO:0017076	purine nucleotide binding	0.0336539626688756
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0336539626688756
GO:0030055	cell-matrix junction	0.0336539626688756
GO:0006760	folic acid and derivative metabolic process	0.035162178684034
GO:0009187	cyclic nucleotide metabolic process	0.0380442230049447
GO:0005912	adherens junction	0.0389687822508273
GO:0000166	nucleotide binding	0.0389687822508273
GO:0048609	reproductive process in a multicellular organism	0.0389687822508273
GO:0032504	multicellular organism reproduction	0.0389687822508273
GO:0043623	cellular protein complex assembly	0.042369104863588
GO:0007565	female pregnancy	0.0433708075059849
GO:0016773	phosphotransferase activity, alcohol group as acceptor	0.0433708075059849
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0433708075059849
GO:0016323	basolateral plasma membrane	0.0433708075059849
GO:0007229	integrin-mediated signaling pathway	0.0433708075059849
GO:0019933	cAMP-mediated signaling	0.0433708075059849
GO:0019205	nucleobase, nucleoside, nucleotide kinase activity	0.0439824022570293

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	1.24e-20	43
endodermal cell	2.58e-13	59
respiratory epithelial cell	1.31e-10	13
epithelial cell	4.08e-10	254
epithelial cell of alimentary canal	1.70e-08	21
general ecto-epithelial cell	1.82e-08	13
skin fibroblast	2.02e-07	23
embryonic cell	2.86e-07	248
ecto-epithelial cell	8.97e-07	33

Uber Anatomy

Ontology term	p-value	n
surface structure	8.25e-12	95
skin of body	1.06e-08	40
integument	1.35e-07	45
integumental system	1.35e-07	45
oral opening	6.31e-07	21
urothelium	8.26e-07	5

Disease

Ontology term	p-value	n
squamous cell carcinoma	8.69e-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
STAT3#6774	4	6.01112285551671	0.00225577915639448	0.0128101418799784

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.