Table 2 The eight performance indices implemented in our tool

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