NOVEL APPLICATION OF POSITIONAL WEIGHT MATRICES FOR TRANSCRIPTION
FACTOR BINDING SITE DISCOVERY
TIME:
3:30 PM
LOCATION:
GMCS 214
SPEAKER:
Scott Kelley
Assistant Professor
Department of Biology
San Diego State University
ABSTRACT:
The characterization and interaction of transcriptional
regulatory
elements is fundamental to understanding how eukaryotic gene networks
operate. Identification of the underlying transcription factors
(TFs) and their target sequences is crucial to characterizing these
regulatory elements. Many computational methods developed to locate
TF binding sites (TFBS) have relied on information from previously
characterized sites. Yet, the majority of TFs do have not binding
site profiles, suggesting these methods may not find uncharacterized
sites. We propose a new approach to identify TFs in a set of
unaligned sequences with no prior binding site information and with
an emphasis on discovering new functional binding sites. Our method
compiles positional weight matrices from a set of regulatory
sequences taken from co-regulated or tissue-specific genes. These
matrices are then used to find statistically over-represented motifs
in the input sequences, relative to the rest of the organism's
intergenic genome. We test our approach on a set of
well-characterized Drosophila development genes. Our results
indicate this method effectively predicts known binding sites and
also identifies DNA regions that contain promising TFBS candidates.
