Coexpression cluster:C3148

Full id: C3148_seminal_parotid_ductus_salivary_submaxillary_papillotubular_breast

Phase1 CAGE Peaks

Hg19::chr11:34535332..34535347,-	p2@ELF5
Hg19::chr11:34645791..34645836,+	p3@EHF
Hg19::chr1:239349935..239349963,-	p@chr1:239349935..239349963 -

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:0008283	cell proliferation	0.0164530039462012
GO:0043565	sequence-specific DNA binding	0.0164530039462012
GO:0003700	transcription factor activity	0.0264787580730052
GO:0030855	epithelial cell differentiation	0.0264787580730052
GO:0002009	morphogenesis of an epithelium	0.0370555220697988
GO:0006355	regulation of transcription, DNA-dependent	0.0439874875106986
GO:0006351	transcription, DNA-dependent	0.0439874875106986
GO:0032774	RNA biosynthetic process	0.0439874875106986
GO:0003677	DNA binding	0.0439874875106986
GO:0045449	regulation of transcription	0.0439874875106986
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0439874875106986
GO:0006350	transcription	0.0439874875106986
GO:0010468	regulation of gene expression	0.0439874875106986
GO:0045893	positive regulation of transcription, DNA-dependent	0.0439874875106986
GO:0031323	regulation of cellular metabolic process	0.0439874875106986
GO:0019222	regulation of metabolic process	0.0439874875106986
GO:0016070	RNA metabolic process	0.0439874875106986
GO:0045941	positive regulation of transcription	0.0445839228449388
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0445839228449388

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
endodermal cell	1.89e-18	59
endo-epithelial cell	1.77e-16	43
respiratory epithelial cell	3.62e-09	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	4.10e-21	169
endoderm	4.10e-21	169
presumptive endoderm	4.10e-21	169
digestive system	3.19e-17	155
digestive tract	3.19e-17	155
primitive gut	3.19e-17	155
subdivision of digestive tract	5.94e-17	129
endodermal part of digestive tract	5.94e-17	129
adult organism	4.75e-15	115
mixed endoderm/mesoderm-derived structure	9.95e-15	130
foregut	1.70e-12	98
respiratory system	5.84e-12	72
immaterial anatomical entity	3.57e-10	126
orifice	2.53e-09	35
oral opening	5.95e-09	21
endo-epithelium	1.17e-08	82
anatomical space	1.84e-08	104
respiratory tract	1.20e-07	53
trunk region element	7.90e-07	107

Disease

Ontology term	p-value	n
adenocarcinoma	1.42e-09	25
carcinoma	2.38e-09	106
squamous cell carcinoma	6.36e-07	14

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.