Table 2 Pathways analysis for joint gender, female, and male Smokers vs Never-smokers. Protein details are provided in Additional file 1: Tables S1, S2, S3 and S4

Pathway (No. of proteins in pathway)

Hits^a

p-value

pFDR

Hits

p-value

pFDR

Hits

p-value

pFDR

Ribosome (180)

58(56↓)

3.4 × 10⁻³⁴

7.1 × 10⁻³²

53^b(51↓)

1.2 × 10⁻³⁴

2.6 × 10⁻³²

37(36↓)

3.7 × 10⁻²⁶

6.7 × 10⁻²⁴

Oxidative phosphorylation (187)

32(31↑)

9.0 × 10⁻¹³

9.5 × 10⁻¹¹

17(16↑)

2.1 × 10⁻⁵

6.3 × 10⁻⁴

22(21↑)

1.9 × 10⁻¹¹

1.7 × 10⁻⁹

Lysosome (177)

29(22↑)

2.6 × 10⁻¹¹

1.9 × 10⁻⁹

24(18↑)

4.4 × 10⁻¹⁰

4.7 × 10⁻⁸

20(13↑)

1.7 × 10⁻⁹

9.9 × 10⁻⁸

Citrate cycle (TCA cycle) (43)

15(15↑)

2.9 × 10⁻¹⁰

1.5 × 10⁻⁸

12(12↑)

1.1 × 10⁻⁸

8.1 × 10⁻⁷

11(11↑)

2.2 × 10⁻⁸

1.0 × 10⁻⁸

Valine, leucine and isoleucine degradation (64)

14(13↑)

1.7 × 10⁻⁷

6.0 × 10⁻⁶

11(11↑)

3.1 × 10⁻⁶

1.0 × 10⁻⁴

7(7↑)

6.0 × 10⁻⁴

6.0 × 10⁻³

Pyruvate metabolism (52)

12(10↑)

7.9 × 10⁻⁷

2.1 × 10⁻⁵

9(9↑)

2.3 × 10⁻⁵

6.0 × 10⁻⁴

8(7↑)

2.6 × 10⁻⁵

6.0 × 10⁻⁴

Phagosome (221)

24(13↑)

1.4 × 10⁻⁶

2.7 × 10⁻⁵

19(11↑)

1.5 × 10⁻⁵

5.0 × 10⁻⁴

17(12↑)

6.5 × 10⁻⁶

2.0 × 10⁻⁴

Fatty acid degradation (60)

10(8↑)

7.6 × 10⁻⁵

1.1 × 10⁻³

7(7↑)

1.6 × 10⁻³

0.026

6(6↑)

3.3 × 10⁻³

0.029

Glycolysis / Gluconeogenesis (101)

13(9↑)

7.7 × 10⁻⁵

1.1 × 10⁻³

11(11↑)

1.0 × 10⁻⁴

3.4 × 10⁻³

9(6↑)

2.0 × 10⁻⁴

2.8 × 10⁻³

Peroxisome (109)

13(10↑)

2.0 × 10⁻³

2.0 × 10⁻³

8(5↑)

0.010

0.01

8(6↑)

2.0 × 10⁻³

0.018

Fatty acid metabolism (62)

9(8↑)

4.0 × 10⁻³

5.4 × 10⁻³

8(8↑)

4 .0 × 10⁻⁴

8.0 × 10⁻³

6(6↑)

4.7 × 10⁻³

0.038

Propanoate metabolism (44)

7(5↑)

1.2 × 10⁻³

0.012

5(5↑)

8.0 × 10⁻³

0.10

2(1↑)

0.20

0.68

Fatty acid elongation

5(5↑)

4.9 × 10⁻³

0.04

5(5↑)

1.8 × 10⁻³

0.03

3(3↑)

0.02

0.14

Leukocyte transendothelial migration (166)

13(9↓)

5.3 × 10⁻³

0.045

8(6↓)

0.08

0.46

8(5↓)

0.018

0.13

Antigen presentation by MHC class I(28)^c

6(5↓)

5.3 × 10⁻⁵

2.3 × 10⁻³

4(3↓)

2.1 × 10⁻³

0.045

4(3↓)

5.0 × 10⁻⁴

0.06