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Table 2 Predicted protein-protein interaction pairs using different set of reference genomes.

From: Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling

Reference genome No. clusters >2 No. Co-Conserved predicted pairs No. Co-Conserved proteins
Aerobic 105 3,890 1,233
All 122 9,539 1,539
All (Inverse homology) 129 6,469 1,557
High GC Gram positive 27 4,237 1,058
Low GC Gram positive 33 34,968 1,325
Motile 88 24,198 1,972
Proteobacteria 101 48,730 2,119
Selected 109 3,839 1,206
  1. Pearson correlation coefficient with confidence 0.8 and E-value of 10-15 were used on binary profile vectors unless noted.