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Table 3 Gene Ontology analysis of hypermethylated with low expression in age-related macular degeneration (AMD)

From: Integrated bioinformatics analysis of aberrantly-methylated differentially-expressed genes and pathways in age-related macular degeneration

Category

Term

Description

GeneRatio

BgRatio

P value

Q value

GeneSymbol

Count

Hypermethylated with low expression

 GOTERM_BP

GO:0051028

mRNA transport

7/141

151/18493

0.00016

0.11773

DHX9/HNRNPA3/NUP58/SLU7/SMG1/SRSF11/YTHDC1

7

 GOTERM_BP

GO:0042698

ovulation cycle

5/141

68/18493

0.00017

0.11773

ADAMTS1/ADNP/PAM/SGPL1/TGFB2

5

 GOTERM_BP

GO:0022602

ovulation cycle process

4/141

47/18493

0.00045

0.11773

ADAMTS1/PAM/SGPL1/TGFB2

4

 GOTERM_BP

GO:0060021

roof of mouth development

5/141

89/18493

0.00060

0.11773

CHD7/FOXE1/MEF2C/SGPL1/TGFB2

5

 GOTERM_BP

GO:0021513

spinal cord dorsal/ventral patterning

3/141

22/18493

0.00060

0.11773

INTU/PAX6/SOX1

3

 GOTERM_CC

GO:0016607

nuclear speck

12/146

382/19659

0.00003

0.00790

BAZ2A/DPP3/FAM76B/MAPT/MEF2C/PNISR/SLU7/SREK1/SRSF11/TARDBP/WAC/YTHDC1

12

 GOTERM_CC

GO:0043025

neuronal cell body

12/146

483/19659

0.00027

0.03616

ADNP/CCK/CKB/GRK4/KCND3/MAPT/MPL/PAM/PDE10A/PTPRF/RTN4RL1/TGFB2

12

 GOTERM_CC

GO:0044441

ciliary part

9/146

441/19659

0.00575

0.36035

AHI1/CEP126/CEP131/DYNC2H1/GRK4/INTU/MLF1/NEK8/NIN

9

 GOTERM_CC

GO:0001669

acrosomal vesicle

4/146

106/19659

0.00808

0.36035

CEP131/FLOT2/SPAG8/SV2B

4

 GOTERM_CC

GO:1990351

transporter complex

7/146

333/19659

0.01232

0.36035

ABCD4/GRIK1/GRIN2C/KCND3/PDE4D/PEX13/STX1A

7

 GOTERM_MF

GO:0003680

AT DNA binding

2/141

10/17632

0.00274

0.26873

MAPT/MEF2C

2

 GOTERM_MF

GO:0042578

phosphoric ester hydrolase activity

9/141

369/17632

0.00290

0.26873

CTDSP1/PDE10A/PDE4D/PDPR/PFKFB2/PLPP2/PPP3CA/PTPDC1/PTPRF

9

 GOTERM_MF

GO:0044325

ion channel binding

5/141

125/17632

0.00332

0.26873

KCND3/PDE4D/SLC8A1/STX1A/YWHAZ

5

 GOTERM_MF

GO:0001046

core promoter sequence-specific DNA binding

3/141

38/17632

0.00344

0.26873

BAZ2A/H3F3A/PAX6

3

 GOTERM_MF

GO:0004721

phosphoprotein phosphatase activity

6/141

182/17632

0.00346

0.2687

CTDSP1/PDPR/PLPP2/PPP3CA/PTPDC1/PTPRF

6

  1. Table 3. Gene ontology (GO) pathway enrichment analyses were performed for the selected genes. The cut-off criterion was P < 0.05. The top 5 GO terms in each category in which the 153 hyper-methylated, low-expression genes were significantly involved are shown. They were enriched in the biological process of mRNA transport, etc. The cellular component category revealed enrichment in nuclear speck, neuronal cell body, etc. The molecular function category indicated enrichment in DNA binding and phosphoric ester hydrolase activity
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BMC Ophthalmology

ISSN: 1471-2415

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