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Table 3 Association analyses between the differentially expressed genes (DEGs) in ASD and the human Alu-inserted gene lists

From: Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder

Insertion type

Comparison

GEO datasets

All differentially expressed genes

Upregulated genes

Downregulated genes

P value

Genes (n)

P value

Genes (n)

P value

Genes (n)

All insertion

ASD vs. control

GSE15402

0.799

215

0.926

100

0.799

116

GSE18123

< 0.00005

1492

1.000

255

< 0.00005

1245

GSE25507

0.012

869

0.256

522

< 0.00005

355

GSE42133

< 0.00005

1001

0.015

387

< 0.00005

624

GSE6575

< 0.00005

388

0.955

123

< 0.00005

266

Intronic

ASD vs. control

GSE15402

0.784

212

0.926

99

0.784

114

GSE18123

< 0.00005

1476

0.970

252

< 0.00005

1231

GSE25507

0.007

860

0.322

516

< 0.00005

352

GSE42133

< 0.00005

985

0.012

382

< 0.00005

613

GSE6575

< 0.00005

382

0.882

119

< 0.00005

264

Exonized

ASD vs. control

GSE15402

1.000

15

0.933

6

0.933

9

GSE18123

0.009

102

0.926

14

0.003

88

GSE25507

0.825

45

0.008

17

0.012

28

GSE42133

0.008

75

0.306

27

0.015

49

GSE6575

0.006

33

1.000

7

< 0.00005

26

Exonic

ASD vs. control

GSE15402

0.450

19

0.904

10

0.426

9

GSE18123

0.001

177

0.306

21

< 0.00005

158

GSE25507

0.426

78

0.136

46

0.662

33

GSE42133

< 0.00005

148

0.799

43

< 0.00005

106

GSE6575

0.034

48

0.715

16

0.013

33

Promoter

ASD vs. control

GSE15402

0.933

6

0.436

1

0.799

5

GSE18123

0.240

37

0.898

8

0.268

29

GSE25507

0.135

22

0.033

11

0.937

11

GSE42133

0.831

35

0.447

19

0.255

16

GSE6575

0.466

16

0.716

3

0.123

13

  1. The list of DEGs from each gene expression profiling study was overlapped with the lists of Alu-inserted genes. Alu-inserted genes were categorized into five types of Alu insertions which included exonized, exonic, intronic, promoter, and combined insertion types. Fisher’s exact test with Benjamini-Hochberg correction (FDR = 0.05) was used to determine the association the DEGs and Alu-inserted genes, and P values of less than 0.05 were considered significant. The number of DEGs and adjusted P values are shown