Coexpression cluster:C360

Full id: C360_Placental_Amniotic_amniotic_teratocarcinoma_chorionic_neuroblastoma_H9

Phase1 CAGE Peaks

Hg19::chr11:1971324..1971344,+	p@chr11:1971324..1971344 +
Hg19::chr11:1982869..1982890,+	p@chr11:1982869..1982890 +
Hg19::chr11:62370454..62370468,-	p@chr11:62370454..62370468 -
Hg19::chr11:62370475..62370497,-	p@chr11:62370475..62370497 -
Hg19::chr11:62370516..62370535,-	p@chr11:62370516..62370535 -
Hg19::chr14:104202647..104202662,-	p@chr14:104202647..104202662 -
Hg19::chr14:24729174..24729183,-	p17@TGM1
Hg19::chr17:37824217..37824226,+	p12@PNMT
Hg19::chr17:37824259..37824278,+	p1@PNMT
Hg19::chr19:1513576..1513590,-	p2@ADAMTSL5
Hg19::chr19:36592925..36592948,+	p@chr19:36592925..36592948 +
Hg19::chr19:36592959..36592975,+	p@chr19:36592959..36592975 +
Hg19::chr19:36592982..36592993,+	p@chr19:36592982..36592993 +
Hg19::chr1:161044552..161044633,-	p2@PVRL4
Hg19::chr1:27339317..27339375,-	p1@FAM46B
Hg19::chr20:61288222..61288232,+	p14@SLCO4A1
Hg19::chr20:61288249..61288259,+	p12@SLCO4A1
Hg19::chr4:177592751..177592777,-	p@chr4:177592751..177592777 -
Hg19::chr5:153854787..153854796,-	p@chr5:153854787..153854796 -
Hg19::chr5:153854814..153854825,-	p@chr5:153854814..153854825 -
Hg19::chr5:153855055..153855066,-	p@chr5:153855055..153855066 -
Hg19::chr5:153855212..153855222,-	p@chr5:153855212..153855222 -
Hg19::chr5:153857778..153857794,-	p1@HAND1
Hg19::chr5:153857800..153857812,-	p2@HAND1
Hg19::chr5:153857819..153857824,-	p3@HAND1
Hg19::chr5:153858046..153858049,+	p@chr5:153858046..153858049 +
Hg19::chr5:153858071..153858085,+	p@chr5:153858071..153858085 +
Hg19::chr7:29603436..29603471,+	p1@PRR15
Hg19::chr7:29603477..29603510,+	p2@PRR15
Hg19::chr7:29603521..29603533,+	p4@PRR15
Hg19::chr7:29603552..29603566,+	p5@PRR15

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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GO ID	GO name	FDR corrected p-value
GO:0048729	tissue morphogenesis	0.00775487924830703
GO:0006576	biogenic amine metabolic process	0.00775487924830703
GO:0006575	amino acid derivative metabolic process	0.00775487924830703
GO:0004603	phenylethanolamine N-methyltransferase activity	0.0082935947250677
GO:0043163	cell envelope organization and biogenesis	0.0110571497501241
GO:0015349	thyroid hormone transmembrane transporter activity	0.0110571497501241
GO:0009888	tissue development	0.0351980101711255
GO:0042423	catecholamine biosynthetic process	0.0351980101711255
GO:0009887	organ morphogenesis	0.0351980101711255
GO:0042403	thyroid hormone metabolic process	0.0351980101711255
GO:0005913	cell-cell adherens junction	0.0351980101711255
GO:0003810	protein-glutamine gamma-glutamyltransferase activity	0.0351980101711255
GO:0001707	mesoderm formation	0.0351980101711255
GO:0030054	cell junction	0.0351980101711255
GO:0048332	mesoderm morphogenesis	0.0351980101711255
GO:0001704	formation of primary germ layer	0.0351980101711255
GO:0045229	external encapsulating structure organization and biogenesis	0.0388545276905836
GO:0001533	cornified envelope	0.0388545276905836
GO:0007369	gastrulation	0.0388545276905836
GO:0006519	amino acid and derivative metabolic process	0.0388545276905836
GO:0018149	peptide cross-linking	0.0388545276905836
GO:0006584	catecholamine metabolic process	0.0388545276905836
GO:0018958	phenol metabolic process	0.0388545276905836
GO:0030216	keratinocyte differentiation	0.0413619195937827
GO:0009308	amine metabolic process	0.0432556527482064
GO:0042401	biogenic amine biosynthetic process	0.0432556527482064
GO:0031424	keratinization	0.0449337123578184
GO:0006807	nitrogen compound metabolic process	0.0449337123578184
GO:0016755	transferase activity, transferring amino-acyl groups	0.0454419119423075
GO:0042398	amino acid derivative biosynthetic process	0.0454419119423075
GO:0007275	multicellular organismal development	0.0454419119423075
GO:0007498	mesoderm development	0.0454419119423075
GO:0009913	epidermal cell differentiation	0.048575240672889
GO:0008170	N-methyltransferase activity	0.048575240672889

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
extraembryonic cell	1.48e-43	19
placental epithelial cell	8.05e-27	3
amniotic epithelial cell	2.66e-18	2
amnion mesenchymal stem cell	5.20e-16	5
chorionic membrane mesenchymal stem cell	2.85e-12	3

Uber Anatomy

Ontology term	p-value	n
extraembryonic membrane	5.05e-72	14
membranous layer	5.05e-72	14
chorion	1.30e-43	7
extraembryonic structure	2.56e-41	24
placenta	8.23e-35	4
allantois	8.23e-35	4
amnion	1.57e-30	7
somatic layer of lateral plate mesoderm	1.04e-26	8
organ component layer	1.57e-16	66
uterus	4.40e-14	21
embryonic uterus	2.01e-13	22
internal female genitalia	2.01e-13	22
acellular anatomical structure	2.85e-12	3
egg chorion	2.85e-12	3
internal genitalia	9.35e-12	25
reproductive structure	3.61e-10	59
reproductive system	3.61e-10	59
reproductive organ	3.93e-10	48
tonsil	2.46e-09	1
mucosa-associated lymphoid tissue	2.46e-09	1
lymphoid tissue	2.46e-09	1
tonsillar ring	2.46e-09	1
female reproductive organ	8.77e-08	37
female reproductive system	8.77e-08	37
mixed endoderm/mesoderm-derived structure	3.05e-07	29
female organism	5.65e-07	41

Disease

Ontology term	p-value	n
vascular disease	1.06e-09	1
ischemia	1.06e-09	1
extrinsic cardiomyopathy	1.06e-09	1
myocardial ischemia	1.06e-09	1
myocardial infarction	1.06e-09	1

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
CTBP2#1488	3	6.0693871296124	0.0130502893883174	0.0463008857365383

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.