Genes which are co-expressed in tissues or processes are often regulated by the same transcription factors. In this thesis, the analysis of transcription factors predicted to regulate a gene is conducted to attempt to discover co-regulated, possibly co-expressed, genes. The initial problem tackled in the thesis is to determine an accurate method of predicting transcription factor binding sites (TFBS), and therefore regulatory transcription factors. Three TFBS prediction methods are developed; one consensus method combining pairs of prediction algorithms, one consensus method combining 6 algorithms through a Naïve Bayes classifier and a phylogenetic footprinting method combining data from multiple organisms using a Naïve Bayes classifier.