Coexpression cluster:C2129

Full id: C2129_Placental_amniotic_Keratinocyte_Corneal_Gingival_Mammary_tongue

Phase1 CAGE Peaks

Hg19::chr11:392573..392586,+	p4@PKP3
Hg19::chr11:392587..392618,+	p2@PKP3
Hg19::chr11:392625..392628,+	p13@PKP3
Hg19::chr11:507175..507178,-	p6@RNH1

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:0008428	ribonuclease inhibitor activity	0.00359113989022636
GO:0032311	angiogenin-PRI complex	0.00359113989022636
GO:0030057	desmosome	0.0119690567876416
GO:0006402	mRNA catabolic process	0.0240959689759813
GO:0045765	regulation of angiogenesis	0.0240959689759813
GO:0006401	RNA catabolic process	0.0240959689759813
GO:0014704	intercalated disc	0.0240959689759813
GO:0043296	apical junction complex	0.0413135693345607
GO:0016327	apicolateral plasma membrane	0.0413135693345607
GO:0001525	angiogenesis	0.0413135693345607
GO:0048514	blood vessel morphogenesis	0.0413135693345607
GO:0048646	anatomical structure formation	0.0413135693345607
GO:0001568	blood vessel development	0.0413135693345607
GO:0001944	vasculature development	0.0413135693345607
GO:0005911	intercellular junction	0.0413135693345607

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	5.10e-14	43
endodermal cell	2.23e-10	59
epithelial cell	1.23e-08	254
epithelial cell of alimentary canal	3.30e-07	21

Uber Anatomy

Ontology term	p-value	n
extraembryonic membrane	1.77e-08	14
membranous layer	1.77e-08	14
surface structure	2.19e-07	95
respiratory system	2.21e-07	72
orifice	3.56e-07	35
reproductive structure	4.46e-07	59
reproductive system	4.46e-07	59
endoderm-derived structure	6.10e-07	169
endoderm	6.10e-07	169
presumptive endoderm	6.10e-07	169

Disease

Ontology term	p-value	n
squamous cell carcinoma	3.50e-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.