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Table 1 Details of the yeast MIPS datasets used in optimization studies *

From: A domain-based approach to predict protein-protein interactions

No of Parameters/Data Seta   PPI Retained Interactions
103 Inclusive Positive 342
   Negative 14,402
867 Inclusive Positive 1,882
   Negative 79,413
344 a Closed Positive 435
   Negative 3,139
2466 Inclusive Positive 2,308
   Negative 162,115
1216 a Closed Positive 734
   Negative 13,146
5095 Inclusive Positive 2,666
   Negative 243,866
3060 a Closed Positive 1,448
   Negative 25,651
  1. * Starting yeast dataset was obtained from Munich Information Center for Protein Sequences (MIPS) site [35] and it contained 8250 positive and ~2 million negative protein-protein interactions [12]. Retained interactions column report the number of entries for the sets after the original dataset is filtered according to the domain pairs included as optimization parameters. Further details can be found in the Methods section. a These are the closed set versions of the 867, 2466, and 5095 parameter inclusive sets. As explained in the Methods section, during filtering to obtain the closed PPI sets, occurrence of some of the domain pairs are nullified and these parameters cannot be truly optimized during the GA runs. So these closed sets are a subset of their corresponding inclusive sets.