Coexpression cluster:C640

Full id: C640_amniotic_salivary_chorionic_Keratinocyte_Urothelial_Prostate_Mammary

Phase1 CAGE Peaks

Hg19::chr10:105791560..105791576,-	p7@COL17A1
Hg19::chr10:105819927..105819974,+	p@chr10:105819927..105819974 +
Hg19::chr10:105824227..105824253,+	p@chr10:105824227..105824253 +
Hg19::chr10:105824310..105824328,-	p12@COL17A1
Hg19::chr10:105830210..105830215,-	p@chr10:105830210..105830215 -
Hg19::chr10:105830255..105830294,-	p@chr10:105830255..105830294 -
Hg19::chr10:105836085..105836093,-	p@chr10:105836085..105836093 -
Hg19::chr10:105836134..105836160,-	p@chr10:105836134..105836160 -
Hg19::chr10:105836165..105836175,-	p@chr10:105836165..105836175 -
Hg19::chr10:105845551..105845581,-	p2@COL17A1
Hg19::chr10:105845611..105845645,-	p1@COL17A1
Hg19::chr10:105845674..105845722,-	p3@COL17A1
Hg19::chr6:7586117..7586135,+	p9@DSP

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
5.75814629513173e-06	0.00364490660481838	2	69	Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244

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:0008544	epidermis development	0.000567241222222142
GO:0007398	ectoderm development	0.000567241222222142
GO:0005911	intercellular junction	0.000567241222222142
GO:0009888	tissue development	0.00132564708271702
GO:0030054	cell junction	0.00210012693832474
GO:0005913	cell-cell adherens junction	0.00841721083028887
GO:0048513	organ development	0.010626908581125
GO:0001533	cornified envelope	0.0106819675426817
GO:0018149	peptide cross-linking	0.0112207999992292
GO:0030216	keratinocyte differentiation	0.0116516829588302
GO:0048731	system development	0.0133844707925655
GO:0005912	adherens junction	0.0174713479979979
GO:0048856	anatomical structure development	0.017675968976235
GO:0044459	plasma membrane part	0.0201424468047065
GO:0007275	multicellular organismal development	0.0201424468047065
GO:0005200	structural constituent of cytoskeleton	0.0206164785855694
GO:0030674	protein binding, bridging	0.0207715838525679
GO:0007160	cell-matrix adhesion	0.0210321636243287
GO:0031589	cell-substrate adhesion	0.0210321636243287
GO:0006817	phosphate transport	0.027723638321343
GO:0032502	developmental process	0.0304983850393752
GO:0005886	plasma membrane	0.0363123514587199
GO:0032501	multicellular organismal process	0.0363123514587199
GO:0005882	intermediate filament	0.0365527498515394
GO:0045111	intermediate filament cytoskeleton	0.0365527498515394
GO:0015698	inorganic anion transport	0.0387074078945368
GO:0006820	anion transport	0.0462624270633432

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
epithelial cell	5.23e-28	254
endo-epithelial cell	1.65e-19	43
endodermal cell	8.54e-19	59
epithelial cell of alimentary canal	2.00e-10	21
respiratory epithelial cell	1.88e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	8.03e-24	169
endoderm	8.03e-24	169
presumptive endoderm	8.03e-24	169
digestive system	3.99e-18	155
digestive tract	3.99e-18	155
primitive gut	3.99e-18	155
mixed endoderm/mesoderm-derived structure	5.36e-16	130
subdivision of digestive tract	1.51e-15	129
endodermal part of digestive tract	1.51e-15	129
respiratory system	9.80e-15	72
foregut	1.18e-11	98
organ	2.70e-10	511
respiratory tract	5.68e-10	53
extraembryonic membrane	7.07e-10	14
membranous layer	7.07e-10	14
immaterial anatomical entity	4.43e-09	126
endo-epithelium	1.08e-08	82
anatomical space	1.29e-08	104
reproductive structure	1.41e-08	59
reproductive system	1.41e-08	59
orifice	1.64e-08	35
reproductive organ	2.05e-08	48
surface structure	3.07e-08	95
segment of respiratory tract	3.91e-08	46
oral opening	5.36e-08	21
internal genitalia	6.07e-08	25
multi-cellular organism	6.45e-08	659
organ component layer	1.34e-07	57
embryonic uterus	4.95e-07	22
female organism	5.90e-07	41
respiratory primordium	6.85e-07	38
endoderm of foregut	6.85e-07	38
internal female genitalia	8.15e-07	22

Disease

Ontology term	p-value	n
carcinoma	1.97e-20	106
cell type cancer	1.29e-14	143
squamous cell carcinoma	1.18e-09	14
adenocarcinoma	9.98e-08	25

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)
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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.