Coexpression cluster:C2355

Full id: C2355_Reticulocytes_chronic_acute_CD34_skeletal_Skeletal_leukemia

Phase1 CAGE Peaks

Hg19::chr15:91445275..91445289,+	p28@MAN2A2
Hg19::chr1:3689325..3689369,+	p2@LOC388588
Hg19::chr2:190446738..190446765,-	p3@SLC40A1
Hg19::chr9:20382446..20382493,-	p4@MLLT3

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:0004572	mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity	0.0185441379597977
GO:0005381	iron ion transmembrane transporter activity	0.0278129317154168
GO:0004559	alpha-mannosidase activity	0.0308996186091742
GO:0006013	mannose metabolic process	0.0347569542511018
GO:0015924	mannosyl-oligosaccharide mannosidase activity	0.0463153233814627
GO:0046915	transition metal ion transmembrane transporter activity	0.0463153233814627
GO:0015923	mannosidase activity	0.0463153233814627
GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity	0.0479684279760137
GO:0055072	iron ion homeostasis	0.0479684279760137
GO:0006879	cellular iron ion homeostasis	0.0479684279760137
GO:0006826	iron ion transport	0.0479684279760137

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.87e-14	115

Disease

Ontology term	p-value	n
myeloid leukemia	6.20e-09	31

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)
{{{tfbs_overrepresentation_jaspar}}}

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.0487143149255538
GATA1#2623	3	10.1702311078503	0.00151515816849827	0.00966183929416236
GTF2B#2959	2	15.9719149671621	0.00563658572353722	0.0254707241424586
SMARCA4#6597	2	78.382951653944	0.000241873026518346	0.00263135177255724
TAL1#6886	2	14.9343083387201	0.00642807757788807	0.0279446384514258

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.