Coexpression cluster:C1825

Full id: C1825_pancreas_Hepatocyte_liver_colon_gastric_hepatoma_hepatoblastoma

Phase1 CAGE Peaks

Hg19::chr19:46367576..46367592,+	p1@FOXA3
Hg19::chr1:199996702..199996732,+	p5@NR5A2
Hg19::chr1:199996733..199996781,+	p1@NR5A2
Hg19::chr6:107235378..107235418,-	p1@ENST00000430094
Hg19::chrX:2882296..2882356,-	p1@ARSE

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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p.value	FDR	nGenes	nPathway	Name
2.20782089021958e-06	0.00139755062350899	2	25	Maturity onset diabetes of the young (KEGG):04950
4.73033289875392e-05	0.0149715036245562	2	114	Regulation of beta-cell development (Reactome):REACT_13698

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:0003702	RNA polymerase II transcription factor activity	0.0105280880666253
GO:0001678	cell glucose homeostasis	0.0105280880666253
GO:0042592	homeostatic process	0.0105280880666253
GO:0009267	cellular response to starvation	0.0105280880666253
GO:0031669	cellular response to nutrient levels	0.0105280880666253
GO:0004065	arylsulfatase activity	0.0105280880666253
GO:0042594	response to starvation	0.0105280880666253
GO:0031668	cellular response to extracellular stimulus	0.0105280880666253
GO:0042593	glucose homeostasis	0.0105280880666253
GO:0033554	cellular response to stress	0.0105280880666253
GO:0033500	carbohydrate homeostasis	0.0105280880666253
GO:0043565	sequence-specific DNA binding	0.0130242900715327
GO:0051716	cellular response to stimulus	0.0130242900715327
GO:0065008	regulation of biological quality	0.0130242900715327
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0130242900715327
GO:0008484	sulfuric ester hydrolase activity	0.0144693029843891
GO:0003704	specific RNA polymerase II transcription factor activity	0.016593720844225
GO:0031667	response to nutrient levels	0.0238504556699512
GO:0003700	transcription factor activity	0.0238504556699512
GO:0009991	response to extracellular stimulus	0.0238504556699512
GO:0048856	anatomical structure development	0.0383789720749396
GO:0003707	steroid hormone receptor activity	0.0383789720749396
GO:0007275	multicellular organismal development	0.0459567706342884
GO:0004879	ligand-dependent nuclear receptor activity	0.0459567706342884

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
kidney cell	2.69e-07	18
kidney epithelial cell	2.69e-07	18

Uber Anatomy

Ontology term	p-value	n
abdomen element	4.27e-13	55
abdominal segment element	4.27e-13	55
abdominal segment of trunk	7.80e-11	61
abdomen	7.80e-11	61
trunk region element	7.35e-10	107
immaterial anatomical entity	8.50e-10	126
kidney	2.32e-09	27
kidney mesenchyme	2.32e-09	27
kidney rudiment	2.32e-09	27
kidney field	2.32e-09	27
epithelium of foregut-midgut junction	9.61e-08	25
anatomical boundary	9.61e-08	25
hepatobiliary system	9.61e-08	25
foregut-midgut junction	9.61e-08	25
septum transversum	9.61e-08	25
duct	1.37e-07	26
digestive system	1.46e-07	155
digestive tract	1.46e-07	155
primitive gut	1.46e-07	155
sac	1.88e-07	26
digestive tract diverticulum	2.19e-07	23
gastrointestinal system	2.90e-07	35
cavitated compound organ	3.75e-07	32
intestine	5.03e-07	27
mesonephros	5.62e-07	18
pronephros	5.62e-07	18
nephrogenic cord	5.62e-07	18
pronephric mesoderm	5.62e-07	18
rostral part of nephrogenic cord	5.62e-07	18
presumptive pronephric mesoderm	5.62e-07	18
epithelial sac	7.41e-07	25
hepatic diverticulum	9.02e-07	22
liver primordium	9.02e-07	22
organ	9.06e-07	511

Disease

Ontology term	p-value	n
carcinoma	5.76e-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.