Coexpression cluster:C318

Full id: C318_hepatoma_Intestinal_bile_small_colon_Prostate_endometrial

Phase1 CAGE Peaks

Hg19::chr10:5048261..5048285,-	p@chr10:5048261..5048285 -
Hg19::chr10:5135981..5136010,+	p6@AKR1C3
Hg19::chr11:111154870..111154887,+	p2@C11orf53
Hg19::chr11:111154907..111154928,+	p1@C11orf53
Hg19::chr11:111154934..111154946,+	p3@C11orf53
Hg19::chr11:111154964..111154975,+	p4@C11orf53
Hg19::chr11:111175739..111175773,-	p6@C11orf92
Hg19::chr11:111175775..111175789,-	p7@C11orf92
Hg19::chr11:111176063..111176079,-	p8@C11orf92
Hg19::chr11:111176084..111176102,-	p9@C11orf92
Hg19::chr11:111176104..111176114,-	p11@C11orf92
Hg19::chr11:69715346..69715355,-	p@chr11:69715346..69715355 -
Hg19::chr11:69715376..69715382,-	p@chr11:69715376..69715382 -
Hg19::chr11:69715408..69715418,-	p@chr11:69715408..69715418 -
Hg19::chr14:23445970..23445991,-	p6@AJUBA
Hg19::chr14:96734892..96734925,-	p1@ENST00000553638
Hg19::chr16:57640858..57640869,-	p@chr16:57640858..57640869 -
Hg19::chr19:41509967..41509988,+	p3@CYP2B6
Hg19::chr19:41510133..41510160,+	p@chr19:41510133..41510160 +
Hg19::chr1:197928283..197928310,+	p@chr1:197928283..197928310 +
Hg19::chr3:30226342..30226387,-	p@chr3:30226342..30226387 -
Hg19::chr4:72468240..72468271,+	p@chr4:72468240..72468271 +
Hg19::chr5:1201465..1201468,+	p11@SLC6A19
Hg19::chr5:1201536..1201542,+	p4@SLC6A19
Hg19::chr5:1202241..1202252,-	p@chr5:1202241..1202252 -
Hg19::chr5:68339691..68339711,-	p1@ENST00000479830
Hg19::chr6:132935900..132935911,-	p@chr6:132935900..132935911 -
Hg19::chr7:107875370..107875381,-	p@chr7:107875370..107875381 -
Hg19::chr8:100519343..100519351,+	p@chr8:100519343..100519351 +
Hg19::chr8:100519383..100519390,+	p@chr8:100519383..100519390 +
Hg19::chr8:17767866..17767892,-	p4@FGL1
Hg19::chr9:22113541..22113546,+	p3@CDKN2B-AS
Hg19::chr9:22113608..22113615,+	p17@CDKN2B-AS
Hg19::chr9:38437671..38437689,+	p@chr9:38437671..38437689 +
Hg19::chr9:38437690..38437712,+	p@chr9:38437690..38437712 +
Hg19::chr9:38437716..38437729,+	p@chr9:38437716..38437729 +
Hg19::chr9:38437744..38437747,+	p@chr9:38437744..38437747 +

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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p.value	FDR	nGenes	nPathway	Name
6.26588234213711e-05	0.0287703396869713	2	59	Arachidonic acid metabolism (KEGG):00590
9.0901547194222e-05	0.0287703396869713	2	71	Metabolism of xenobiotics by cytochrome P450 (KEGG):00980

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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GO ID	GO name	FDR corrected p-value
GO:0047017	prostaglandin-F synthase activity	0.00874172177855952
GO:0047026	3-alpha-hydroxysteroid dehydrogenase (A-specific) activity	0.00874172177855952
GO:0047045	testosterone 17-beta-dehydrogenase (NADP+) activity	0.00874172177855952
GO:0047115	trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity	0.00874172177855952
GO:0050327	testosterone 17-beta-dehydrogenase activity	0.0093240915001036
GO:0005577	fibrinogen complex	0.0165019362595048
GO:0004033	aldo-keto reductase activity	0.0165019362595048
GO:0015804	neutral amino acid transport	0.0165019362595048
GO:0016628	oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor	0.0165019362595048
GO:0006693	prostaglandin metabolic process	0.0165019362595048
GO:0006692	prostanoid metabolic process	0.0165019362595048
GO:0015175	neutral amino acid transmembrane transporter activity	0.0165019362595048
GO:0006118	electron transport	0.0201970832734816
GO:0050381	unspecific monooxygenase activity	0.0216241942435844
GO:0016229	steroid dehydrogenase activity	0.024833518960349
GO:0006091	generation of precursor metabolites and energy	0.0272454932255383
GO:0016712	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	0.0306091097628793
GO:0006690	icosanoid metabolic process	0.0306091097628793
GO:0005328	neurotransmitter:sodium symporter activity	0.0306091097628793
GO:0005326	neurotransmitter transporter activity	0.0308192896656132
GO:0015171	amino acid transmembrane transporter activity	0.034874355006795
GO:0006865	amino acid transport	0.0369765176591999
GO:0006836	neurotransmitter transport	0.037764746818911
GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	0.037764746818911
GO:0015837	amine transport	0.037764746818911
GO:0015370	solute:sodium symporter activity	0.037764746818911
GO:0046943	carboxylic acid transmembrane transporter activity	0.037764746818911
GO:0046942	carboxylic acid transport	0.037764746818911
GO:0015849	organic acid transport	0.037764746818911
GO:0005342	organic acid transmembrane transporter activity	0.037764746818911
GO:0016491	oxidoreductase activity	0.037764746818911
GO:0015294	solute:cation symporter activity	0.0413201004265023

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>

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Cell Type

Ontology term	p-value	n
epithelial cell of prostate	1.12e-17	3
intestinal epithelial cell	1.13e-13	4
endodermal cell	1.42e-08	58

Uber Anatomy

Ontology term	p-value	n
gallbladder	8.00e-18	3
gall bladder primordium	8.00e-18	3
gut epithelium	1.70e-15	54
intestinal mucosa	1.13e-13	4
wall of intestine	1.13e-13	4
gastrointestinal system mucosa	1.13e-13	4
gastrointestinal system epithelium	1.13e-13	4
intestinal epithelium	1.13e-13	4
endo-epithelium	1.66e-10	82
epithelium of foregut-midgut junction	5.06e-09	25
anatomical boundary	5.06e-09	25
hepatobiliary system	5.06e-09	25
foregut-midgut junction	5.06e-09	25
septum transversum	5.06e-09	25
epithelium of mucosa	1.69e-07	8
biliary system	7.91e-07	9
biliary tree	7.91e-07	9
biliary bud	7.91e-07	9
simple columnar epithelium	8.37e-07	9

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
FOXA2#3170	6	3.99412925718896	0.00351570543637029	0.0178509776882238
MAFF#23764	4	6.08814664756164	0.00410937478105608	0.0195864819623364
MAFK#7975	5	3.66226123484188	0.0111349017815124	0.040943492136724

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.