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Table 2 The eight performance indices implemented in our tool

From: PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast

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
  1. *PCTFP is the abbreviation for predicted cooperative TF pair.
  2. Different indices utilizes different data sources and rationales. See our previous study [19] for the details about the mathematics of these eight performance indices.