Table 3 Overlapping DEGs with expression level changes and DMGs with methylation level changes in the combination (BSp + GTPs) treatment group.

From: Systematic integrated analyses of methylomic and transcriptomic impacts of early combined botanicals on estrogen receptor-negative mammary cancer

Gene symbol

Gene expression fold-change (log2FC) (combination vs control)

Average differential expression (combination vs control)

p value for differential expression (combination vs control)

Chromosomal location

Methylation difference (combination vs control)

Aff1

0.432

6.965

3.74E−05

5

− 32.812

Ap1s1

− 0.239

6.395

1.14E−03

5

− 27.815

Ap2s1

− 0.377

6.280

3.02E−04

7

− 27.403

Cdc42bpb

0.349

6.548

3.50E−04

12

− 25.862

Cdk13

0.222

5.982

4.33E−03

13

− 25.380

Clasp2

0.393

5.961

1.72E−03

9

− 26.242

Etl4

0.743

6.713

3.01E−04

2

− 25.050

Get4

− 0.251

5.785

5.27E−03

5

29.204

Gm17018

− 0.262

4.498

3.76E−03

19

− 28.522

Gnaz

− 0.799

1.881

4.23E−04

10

− 25.221

Hsbp1

− 0.303

6.770

3.06E−03

8

− 26.257

Iffo2

0.355

4.731

3.89E−03

4

40.880

Il15ra

0.517

4.863

6.00E−03

2

− 27.794

Kdm2b

0.294

5.574

4.60E−03

5

− 26.947

Mrps12

− 0.295

4.972

2.78E−04

7

− 38.379

Muc5b

2.939

− 4.363

5.78E−04

7

30.468

Mxd3

− 0.767

2.716

1.70E−03

13

− 27.448

Naaladl2

0.728

4.932

6.85E−04

3

− 32.540

Ndufa1

− 0.606

4.841

2.85E−03

X

28.913

Nr2c2

0.431

4.959

1.35E−03

6

− 26.573

Pard3

0.315

6.086

1.18E−03

8

− 31.251

Pdx1

4.119

− 2.107

6.03E−03

5

− 27.076

Phb

− 0.314

7.148

2.80E−03

11

− 26.850

Pomp

− 0.303

7.168

1.40E−03

5

27.013

Prex2

0.616

2.794

5.10E−03

1

− 34.783

Psmb3

− 0.504

6.188

2.35E−03

11

− 28.077

Psmb6

− 0.437

6.948

1.80E−03

11

− 27.334

Psmd9

− 0.248

4.914

3.66E−03

5

− 27.477

Rbx1

− 0.487

6.285

8.75E−04

15

− 25.898

Rpl13

− 0.399

9.816

3.37E−04

8

25.913

Rpl41

− 0.729

9.505

1.32E−03

10

− 27.371

Rps5

− 0.406

9.342

9.02E−05

7

− 26.124

Selenow

− 0.267

6.793

6.07E−03

7

− 29.497

Smim22

− 0.682

4.657

6.17E−04

16

− 27.510

Tmem184a

0.284

6.827

5.77E−03

5

− 29.260

Tnks

0.317

6.279

9.09E−04

8

− 33.032

Trim56

0.378

6.431

1.79E−04

5

− 30.123

Use1

− 0.527

5.689

2.76E−03

8

− 26.789

Tmem132d

1.336

− 0.487

2.70E−04

5

− 31.003

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