Predition Of Shared Regulatory Motifs From Upstream DNA Database For Gallus Gallus

Understanding of transcription factor binding sites (TFBS) allows biologists to have a better insight on the functions of the genes. As such, many TFBS-finding tools have been developed and one of them is the Yeast Motif Finder (YMF). This paper endeavours to explore the possibility of applying YMF on other species (chicken) besides yeast and use it as a mean for independent testing, verification or validation for other tools. The initial step is to obtain sets of co-regulated upstream sequences to be used as input for the YMF. This is done by clustering genes regulated by the same transcription factor and extracting their upstream regions. Following that, the background distribution of the chicken genome was built and fed into the YMF program to calculate the z-scores. Our results show that motifs discovered by YMF share high similarity with those recorded in TRANSFAC. We also discovered some motifs with high z-score predicted by YMF but not recorded in TRANSFAC. These motifs could be a potentially new bind sites or could be overrepresented by chance.