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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)