Skip to main content

Table 3 Pathway enrichment analysis from meta-analysis EWAS results

From: Altered methylation pattern in EXOC4 is associated with stroke outcome: an epigenome-wide association study

Function

Database

Method

Sign CpG cut-off

Type CpGs

ID

Description

Size

P value

Q value

mglm

GO

N/A

No

Promoter

GO:0,030,100

Regulation of endocytosis

242

6.38E-04

5.36E-01

methylRRA

GO

GSA

Nominal

All

GO:0,016,358

Dendrite development

206

3.76E-04

1.62E-02

methylRRA

GO

GSA

Nominal

All

GO:0,048,588

Developmental cell growth

205

1.28E-03

2.75E-02

methylRRA

GO

GSA

No

All

R-HSA-5688426

Deubiquitination

206

1.83E-02

1.83E-02

methylRRA

Reactome

GSA

No

Promoter

R-HSA-5688426

Deubiquitination

206

4.57E-03

1.83E-02

methylRRA

Reactome

GSA

Nominal

Promoter

R-HSA-5688426

Deubiquitination

206

4.72E-03

1.89E-02

methylRRA

Reactome

ORA

Nominal

All

R-HSA-211859

Biological oxidations

203

3.08E-02

3.18E-02

methylRRA

Reactome

ORA

Nominal

All

R-HSA-72203

Processing of Capped Intron-Containing Pre-mRNA

203

3.08E-02

3.18E-02

methylRRA

Reactome

ORA

Nominal

All

R-HSA-162906

HIV infection

205

3.11E-02

3.18E-02

methylRRA

Reactome

ORA

Nominal

All

R-HSA-68882

Mitotic anaphase

209

3.17E-02

3.18E-02

methylRRA

Reactome

ORA

Nominal

All

R-HSA-2555396

Mitotic metaphase and anaphase

210

3.18E-02

3.18E-02

methylRRA

KEGG

ORA

Nominal

All

4510

Focal adhesion

200

3.03E-02

3.05E-02

methylRRA

KEGG

ORA

Nominal

All

4144

Endocytosis

201

3.05E-02

3.05E-02

  1. Description of the significant pathways obtained from MethylGSA analysis using EWAS results from the meta-analysis
  2. Function: Indicates which of the three MethylGSA functions was used; Database: The pathway database used in the analysis; Method: Method used (ORA or GSA) when methylRRA was selected; Sign CpG cut-off: “No” indicates that the analysis was performed including the results from all the CpG sites and “Nominal” indicates that the analysis was performed using the nominally associated CpG sites; type CpGs: “All” indicates that the analysis was performed for all the CpG types, while “promoter” indicates that in the analysis only CpG sites from promotors were analysed; ID: Identifier for the specific pathway from each database; Description: Detail of the pathway; Size: number of genes included in the gene set; and p value: enrichment p value for each gene set; Q value: FDR corrected p value