Performance index type | Index | Data sources used | Rationale |
---|---|---|---|
TF-based | Index1 | Yeast physical PPI data from BioGRID database [27] | Measure the overlap significance of the physical PPI partners of a PCTFP* |
 | Index2 | Yeast physical PPI data from BioGRID database [27] | Measure the shortest path length of a PCTFP in the physical PPI network |
 | Index3 | Yang et al.'s functional similarity scores of any two yeast genes [28] | Measure the functional similarity of a PCTFP |
 | Index4 | Yang et al.'s high-quality benchmark set of 27 cooperative TF pairs in yeast [16] | Measure the overlap significance of the list of PCTFPs from an algorithm and the benchmark set of 27 cooperative TF pairs |
TG-based | Index5 | Balaji et al.'s co-regulatory coefficient dataset of 3459 TF pairs in yeast [29] | Measure the co-regulatory coefficient of a PCTFP |
 | Index6 | Co-expression scores of any two yeast genes from SPELL database [30] and TF-gene documented regulation data from YEASTRACT database [31] | Measure the expression coherence of a PCTFP's common target genes |
 | Index7 | Yang et al.'s functional similarity scores of any two yeast genes [28] and TF-gene documented regulation data from YEASTRACT database [31] | Measure the functional coherence of a PCTFP's common target genes |
 | Index8 | Yeast physical PPI data from BioGRID database [27] and TF-gene documented regulation data from YEASTRACT database [31] | Measure the physical PPI coherence of a PCTFP's common target genes |