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Table 1 Methods under study.

From: Topological comparison of methods for predicting transcriptional cooperativity in yeast

Method Rationale behind the method CTFPs considered in our study
Method N [20] Proteins that are close in the PIN are likely to be co-regulated by the same TFs. Cooperative TF pairs are identified on the basis of the distance between their common target genes in the PIN (as opposed to the distance between genes controlled by either TF). Subcellular localization data was used to filter the PIN. Functional data was used to refine the distances between target genes. Cooperative TF pairs, triads and modules. Members of triads and modules were pairwisely decomposed in an all-vs-all fashion. Gene names were transformed to YPD names. TFs not present in the set of 101 TFs common to all methods were excluded. The number of cooperative TF pairs was 45.
Method B [46] Proteins with similar expression profiles are likely to be co-regulated. Cooperative TF pairs are identified on the basis of their influence on the cell-cycle-dependent co-expression of their common target genes. Significant cooperative TF pairs labeled as significant (PB < 0.001). Gene names were transformed to YPD names and TFs not present in the set of 101 TFs common to all methods were excluded. The number of cooperative TF pairs was 31.
Method T [48] Cooperativity has an influence in the expression level of regulated genes during one or more phases of the cell cycle. First, TFs involved in regulation of the cell cycle are found. Then, TF pairs associated to a target gene more than random expectation are identified. Of these, a cooperative interaction between two TFs is identified based on their influence in the expression level of the target genes regulated by them. Only pairs labeled as "confident" considered. Gene names were transformed to YPD names and TFs not present in the set of 101 TFs common to all methods were excluded. The number of cooperative TF pairs was 15.
Method C [47] DNA-binding sites of cooperative TFs are likely to co-occur in the target genes. Also, cooperative TF pairs are likely to influence changes in the expression profiles of target genes. This influence was measured by means of a dynamic stochastic model on cell-cycle expression data. The method was also applied to gene expression under H2O2 stress. Only TF pairs with p-value < 10-21 were considered. Gene names were transformed to YPD names and TFs not present in the set of 101 TFs common to all methods were excluded. The number of cooperative TF pairs was 46.
  1. Features of the four methods under study. Abbreviations: TF, transcription factor; PIN, protein interaction network.