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Table 1 Data sets investigated in this study

From: Evolution of protein complexes by duplication of homomeric interactions

    Pairwise interactions (%)  
Dataset PPIs/Complexes No. of proteins HD PD F(HD) F(PD) F(HI) F(PI) Description
Pairwise interactions
Yeast [36] 1,011 753 1.9 13.4      Manual curation of small scale data (does not include yeast two hybrid data)
Yeast-large [37] 15,393 4,741 1.8 6.2      Compilation of small- and large-scale data
Worm [39] 2,422 1,726 1.6 3.3      High-throughput (yeast two-hybrid)
Fly [38] 3,384 2,877 2.9 9.1      High-throughput (yeast two-hybrid)
Complexes
MIPS [36] 216 1,185    32 27    Manual curation
TAP [40] 589 1,474    31 30    High-throughput tagging and mass spectometry
HMS-PCI [41] 741 1,758    33 27    High-throughput tagging and mass spectometry
PQS [29] 2509 3,124      85 11 Three-dimensional structures of protein complexes
  1. PPIs/Complexes are the number of protein-protein interactions and protein complexes (for complexes) in the data sets, respectively. HD, homodimers; PD, dimers of paralogous proteins; F(HD) and F(PD) represent the frequency at which the complexes contain homodimers or dimers of paralogous proteins in any of the two S. cerevisiae protein interaction datasets. These numbers were obtained by computationally superimposing the PINs onto the complex data and are significantly higher than expected by chance at p < 10-4 in all cases. F(HI) and F(PI) are the frequency of complexes with homomeric or paralogous interactions, respectively.