Coexpression cluster:C1778

Full id: C1778_tongue_Corneal_Urothelial_salivary_Esophageal_Sebocyte_Keratinocyte

Phase1 CAGE Peaks

Hg19::chr17:39767475..39767486,-	p@chr17:39767475..39767486 -
Hg19::chr17:39768786..39768828,-	p2@KRT16
Hg19::chr17:39769009..39769026,-	p1@KRT16
Hg19::chr1:153003671..153003687,+	p1@SPRR1B
Hg19::chr1:153005015..153005047,+	p3@SPRR1B

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:0008544	epidermis development	0.000458597222349455
GO:0007398	ectoderm development	0.000458597222349455
GO:0045111	intermediate filament cytoskeleton	0.000600703872260292
GO:0005882	intermediate filament	0.000600703872260292
GO:0009888	tissue development	0.000803422474373953
GO:0044430	cytoskeletal part	0.00607856862473792
GO:0048513	organ development	0.00802457504051665
GO:0001533	cornified envelope	0.00802457504051665
GO:0018149	peptide cross-linking	0.00802457504051665
GO:0005856	cytoskeleton	0.00802457504051665
GO:0030216	keratinocyte differentiation	0.00802457504051665
GO:0048731	system development	0.00859968523366381
GO:0031424	keratinization	0.00859968523366381
GO:0009913	epidermal cell differentiation	0.0102953235096531
GO:0048730	epidermis morphogenesis	0.0107846238557537
GO:0048856	anatomical structure development	0.0108800945402962
GO:0048729	tissue morphogenesis	0.012453986215909
GO:0007275	multicellular organismal development	0.0127161911645875
GO:0005200	structural constituent of cytoskeleton	0.0131524584277955
GO:0030674	protein binding, bridging	0.0133756411171839
GO:0043232	intracellular non-membrane-bound organelle	0.0167855209032985
GO:0043228	non-membrane-bound organelle	0.0167855209032985
GO:0032502	developmental process	0.0210957208770382
GO:0032501	multicellular organismal process	0.0263631339504596
GO:0044446	intracellular organelle part	0.028415947659475
GO:0044422	organelle part	0.028415947659475

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	2.97e-19	254
endo-epithelial cell	5.48e-14	43
endodermal cell	2.47e-09	59
respiratory epithelial cell	2.54e-08	13
epithelial cell of alimentary canal	7.60e-08	21

Uber Anatomy

Ontology term	p-value	n
respiratory system	9.27e-14	72
endoderm-derived structure	1.23e-13	169
endoderm	1.23e-13	169
presumptive endoderm	1.23e-13	169
respiratory tract	1.51e-10	53
digestive system	2.30e-09	155
digestive tract	2.30e-09	155
primitive gut	2.30e-09	155
mixed endoderm/mesoderm-derived structure	6.79e-09	130
segment of respiratory tract	6.68e-08	46
surface structure	8.25e-08	95
respiratory primordium	1.35e-07	38
endoderm of foregut	1.35e-07	38
organ component layer	1.97e-07	57
anatomical space	2.14e-07	104
organ	3.24e-07	511
orifice	6.23e-07	35
oral opening	8.41e-07	21
organ part	8.58e-07	219

Disease

Ontology term	p-value	n
squamous cell carcinoma	2.10e-09	14
carcinoma	2.25e-07	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)
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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.