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Table 1 Summary of the results for differential expression and co-regulation analyses

From: Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer

Group

Category

Cutoffs for filtering

LG versus N

HG versus N

HG versus LG

Individual proteins

Total

Quantified in all samples

3642

3642

3642

Differential

q < 0.05; |Log2FC| > 0.5

197

309

33

Up

q < 0.05; Log2FC > 0.5

54a

94b

4

Down

q < 0.05; Log2FC < − 0.5

143c

215c

29

CORUM complexes for differential expression analysis

Total

Quantified subunits ≥ 2; subunit coverage ≥ 50%

852

852

852

Differential

q < 0.05; |Log2FC| > 0.31

54

85

6

Up

q < 0.05; log2FC > 0.31

7

34d

1

Down

q < 0.05; Log2FC <  − 0.31

47e

51e

5

CORUM complexes for differential co-regulation analysis

Total

Quantified subunits ≥ 2; subunit coverage ≥ 50%; PPI coverage ≥ 50%

475

475

475

Differential

q < 0.05; |mean Z score difference| > 0.7

28

22

22

Up

q < 0.05; mean Z score difference > 0.7

20f

17g

10

Down

q < 0.05; mean Z score difference <  − 0.7

8

5

12

  1. aForm three small PPI networks
  2. bForm a large PPI network in cytoplasm and nucleus
  3. cForm a large PPI network mainly in extracellular space, plasma membrane, and cytoplasm
  4. dFour ProTα complexes are involved in the negative regulation of apoptotic process (GO:0043066)
  5. eThirteen integrin protein complexes are involved in cell adhesion (GO:0007155)
  6. fEleven protein complexes are nuclear complexes, of which six are involved in RNA splicing (GO:0008380)
  7. gFour subcomplexes of mitochondrial complex I are involved in oxidative phosphorylation (GO:0006818)