Coexpression cluster:C556

Full id: C556_pharyngeal_Gingival_Retinal_lung_Mallassezderived_Small_mesothelioma

Phase1 CAGE Peaks

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Hg19::chr11:102642814..102642823,-	p@chr11:102642814..102642823 -
Hg19::chr11:102651279..102651288,-	p2@MMP10
Hg19::chr11:102651343..102651365,-	p1@MMP10
Hg19::chr11:102700844..102700849,-	p@chr11:102700844..102700849 -
Hg19::chr14:22659199..22659211,-	p@chr14:22659199..22659211 -
Hg19::chr14:22677969..22677976,-	p@chr14:22677969..22677976 -
Hg19::chr14:22678054..22678089,-	p@chr14:22678054..22678089 -
Hg19::chr14:22678115..22678119,-	p@chr14:22678115..22678119 -
Hg19::chr16:23119386..23119416,-	p@chr16:23119386..23119416 -
Hg19::chr1:211565263..211565280,+	p@chr1:211565263..211565280 +
Id	Short description

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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 ID	GO name	FDR corrected p-value
GO:0007586	digestion	2.61e-2
GO:0030303	stromelysin 2 activity	1.65e-3
GO:0030342	1-alpha,25-dihydroxyvitamin D3 (1,25-(OH)2D3) 24-hydroxylase activity	1.65e-3
GO:0030574	collagen catabolic process	6.89e-3
GO:0032963	collagen metabolic process	6.89e-3
GO:0044236	multicellular organismal metabolic process	6.89e-3
GO:0044243	multicellular organismal catabolic process	6.89e-3
GO:0044254	multicellular organismal protein catabolic process	6.89e-3
GO:0044256	protein digestion	6.89e-3
GO:0044259	multicellular organismal macromolecule metabolic process	6.89e-3

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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

Ontology term	p-value	n
epithelial cell of prostate	2.59e-12	3
endo-epithelial cell	7.58e-08	42
epithelial cell of uterus	8.02e-07	6
stromal cell of endometrium	8.02e-07	6

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Uber Anatomy

Ontology term	p-value	n

Ontology term	p-value	n
pharynx	4.80e-13	11
open tracheal system trachea	6.48e-18	2
tonsil	7.06e-34	1
mucosa-associated lymphoid tissue	7.06e-34	1
lymphoid tissue	7.06e-34	1
tonsillar ring	7.06e-34	1

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Disease

Ontology term	p-value	n

Ontology term	p-value	n
female reproductive endometrioid cancer	8.02e-07	6

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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

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Motifs	-log10(p-value)

Motifs	-log10(p-value)
motif93_TANTMTCTRWAT	2.36
motif4_TGTCTA	2.04
motif140_WTAAATAACG	1.75
motif83_TTWTAAA	1.60
motif148_NTCSYSTYT	1.59
motif120_TTSMTGNNGKTG	1.46
motif144_AAKCMSGT	1.45
motif141_TTAAACGGC	1.35
motif90_TTATATCGC	1.30
motif104_GTWSGMT	1.28

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JASPAR motifs

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Motifs	-log10(p-value)

Motifs	-log10(p-value)
MA0027.1	2.23
MA0101.1	1.89
MA0069.1	1.53
MA0030.1	1.37
MA0108.2	1.23
MA0050.1	1.21
MA0102.2	1.17
MA0154.1	1.15
MA0092.1	1.14
MA0084.1	1.13

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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.