It is broadly known that conserved DNA sequences (e.g. cis-motifs in the upstream region of genes) and conserved sequences in the specific transcription factors that bind to them (i.e. protein domains) play a major role in the DNA binding process. These domain DNA binding interactions and other domain interactions such as protein-protein interactions play a critical role in the gene regulation process. To date, a number of investigations have been made, in first detecting protein domains and then detecting their functions and associated biological processes. With the rapid increase in the number of known DNA and protein sequences locating significant associations between protein domains and DNA motifs has become a valid approach for detecting their roles in the regulation process. Here we present our new approach to detecting associations between protein domains and DNA motifs in Saccharomyces cerevisiae based on Gene Ontology terms which can help biologists to generating different types of hypotheses.