Coexpression cluster:C393

Full id: C393_amniotic_Placental_Amniotic_clear_Basophils_pharyngeal_tonsil

Phase1 CAGE Peaks

Hg19::chr11:1946152..1946161,+	p12@TNNT3
Hg19::chr12:83148856..83148864,+	p@chr12:83148856..83148864 +
Hg19::chr12:8975061..8975072,+	p5@A2ML1
Hg19::chr13:30415684..30415696,-	p@chr13:30415684..30415696 -
Hg19::chr16:70740254..70740259,-	p@chr16:70740254..70740259 -
Hg19::chr1:153520959..153520976,-	p6@S100A3
Hg19::chr21:39670082..39670093,+	p@chr21:39670082..39670093 +
Hg19::chr21:39670125..39670140,+	p@chr21:39670125..39670140 +
Hg19::chr3:134044856..134044890,+	p@chr3:134044856..134044890 +
Hg19::chr3:146323019..146323049,-	p1@PLSCR5
Hg19::chr3:24339226..24339231,-	p@chr3:24339226..24339231 -
Hg19::chr3:54925405..54925424,+	p@chr3:54925405..54925424 +
Hg19::chr3:54925431..54925442,+	p@chr3:54925431..54925442 +
Hg19::chr3:55513517..55513530,-	p@chr3:55513517..55513530 -
Hg19::chr4:38062660..38062664,+	p@chr4:38062660..38062664 +
Hg19::chr5:170210042..170210086,-	p@chr5:170210042..170210086 -
Hg19::chr5:170210721..170210734,+	p1@GABRP
Hg19::chr5:170238215..170238225,+	p@chr5:170238215..170238225 +
Hg19::chr5:170239966..170239982,+	p@chr5:170239966..170239982 +
Hg19::chr5:170241044..170241049,-	p@chr5:170241044..170241049 -
Hg19::chr6:75828835..75828850,-	p21@COL12A1
Hg19::chr6:75828851..75828864,-	p20@COL12A1
Hg19::chr6:75828867..75828885,-	p10@COL12A1
Hg19::chr7:114542043..114542046,-	p@chr7:114542043..114542046 -
Hg19::chr7:14880892..14880938,-	p16@DGKB
Hg19::chr8:143867355..143867390,-	p2@LY6D
Hg19::chr8:8318890..8318903,-	p1@ENST00000521218

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:0005595	collagen type XII	0.0282266369397579
GO:0030020	extracellular matrix structural constituent conferring tensile strength	0.0282266369397579
GO:0005861	troponin complex	0.0344718141264407
GO:0005593	FACIT collagen	0.0344718141264407
GO:0006942	regulation of striated muscle contraction	0.0344718141264407
GO:0030934	anchoring collagen	0.0344718141264407
GO:0005515	protein binding	0.0344718141264407
GO:0030199	collagen fibril organization	0.0344718141264407
GO:0005865	striated muscle thin filament	0.0344718141264407

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
endo-epithelial cell	5.28e-08	43
epithelial cell	4.22e-07	254

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	4.21e-15	169
endoderm	4.21e-15	169
presumptive endoderm	4.21e-15	169
digestive system	4.11e-13	155
digestive tract	4.11e-13	155
primitive gut	4.11e-13	155
organ component layer	1.37e-11	57
mixed endoderm/mesoderm-derived structure	1.72e-11	130
surface structure	2.64e-11	95
extraembryonic membrane	1.71e-10	14
membranous layer	1.71e-10	14
respiratory system	6.57e-10	72
subdivision of digestive tract	6.42e-09	129
endodermal part of digestive tract	6.42e-09	129
organ	4.79e-08	511
mouth	1.41e-07	28
stomodeum	1.41e-07	28
orifice	2.64e-07	35
extraembryonic structure	6.92e-07	24
multi-cellular organism	7.37e-07	659

Disease

Ontology term	p-value	n
carcinoma	8.42e-10	106

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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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.