Even in a simple organism like yeast Saccharomyces cerevisiae, transcription is an extremely complex process. The expression of sets of genes can be turned on or off by the binding of specific transcription factors to the promoter regions of genes. Experimental and computational approaches have been proposed to establish mappings of DNA-binding locations of transcription factors. However, although location data obtained from experimental methods are noisy owing to imperfections in the measuring methods, computational approaches suffer from over-prediction problems owing to the short length of the sequence motifs bound by the transcription factors. Also, these interactions are usually environment-dependent: many regulators only bind to the promoter region of genes under specific environmental conditions. Even more, the presence of regulators at a promoter region indicates binding but not necessarily function: the regulator may act positively, negatively or not act at all. Therefore, identifying true and functional interactions between transcription factors and genes in specific environment conditions and describing the relationship between them are still open problems.