Coexpression cluster:C2461

Full id: C2461_CD8_CD4_Natural_Basophils_CD34_Mesenchymal_uterus

Phase1 CAGE Peaks

Hg19::chr18:47340320..47340479,+	p1@SCARNA17
Hg19::chr18:47340483..47340506,+	p2@SCARNA17
Hg19::chr18:47340573..47340583,+	p@chr18:47340573..47340583 +
Hg19::chr18:47340651..47340714,-	p5@ACAA2

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:0003988	acetyl-CoA C-acyltransferase activity	0.00388555280819498
GO:0016408	C-acyltransferase activity	0.00582832921229247
GO:0006695	cholesterol biosynthetic process	0.00801395266690215
GO:0016126	sterol biosynthetic process	0.00801395266690215
GO:0008203	cholesterol metabolic process	0.0130443558560832
GO:0006694	steroid biosynthetic process	0.0130443558560832
GO:0016125	sterol metabolic process	0.0130443558560832
GO:0006631	fatty acid metabolic process	0.0221177621389561
GO:0008202	steroid metabolic process	0.0221177621389561
GO:0008415	acyltransferase activity	0.0221177621389561
GO:0016747	transferase activity, transferring groups other than amino-acyl groups	0.0221177621389561
GO:0032787	monocarboxylic acid metabolic process	0.0221177621389561
GO:0016746	transferase activity, transferring acyl groups	0.0221177621389561
GO:0008610	lipid biosynthetic process	0.0231051622344452
GO:0006066	alcohol metabolic process	0.0288178499941128
GO:0044255	cellular lipid metabolic process	0.0430648769574944
GO:0019752	carboxylic acid metabolic process	0.0430648769574944
GO:0006082	organic acid metabolic process	0.0430648769574944
GO:0006629	lipid metabolic process	0.0483649073230586
GO:0005739	mitochondrion	0.0485694101024373

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><br>

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Cell Type

Ontology term	p-value	n
mature alpha-beta T cell	6.74e-13	18
alpha-beta T cell	6.74e-13	18
immature T cell	6.74e-13	18
mature T cell	6.74e-13	18
immature alpha-beta T cell	6.74e-13	18
CD8-positive, alpha-beta T cell	9.68e-09	11
T cell	1.36e-08	25
pro-T cell	1.36e-08	25

Uber Anatomy

Ontology term	p-value	n
adult organism	1.95e-15	114
blood	1.05e-07	15
haemolymphatic fluid	1.05e-07	15
organism substance	1.05e-07	15

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
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109277808297142
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186341346740199
SRF#6722	4	13.7971782621678	2.75840773062708e-05	0.000584233106832207

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.