Michael Caudy, Ph.D., Burke Medical Research Institute
Track: System Administration and Infrastructure
Date: Wednesday, February 05
Time: 4:00pm - 4:45pm
Location: California Ballroom C
This talk was co-authored by Lincoln Stein, Cold Springs Harbor Labs, and James Tisdall, Biocomputing Associates.
A set of computational, visualization, and database annotation tools will be presented that allows the identification and analysis of transcriptional regulatory sequences that control neuronal gene expression within a neuronal differentiation pathway.
Computational analysis of transcription regulatory elements (TREs)
Perl scripts using regular expressions for pattern matching are used to search the entire Drosophila (fruit fly) genome for DNA sequences likely to function as transcription regulatory elements (TREs) that control neuronal-specific gene expression during embryonic development. The TREs are clusters of transcription factor binding sites within a small DNA region.
Visualization of TREs relative to known genes in the genome
A web genome browser - GBrowse - is used to graphically display the many hundreds or thousands of potential TREs revealed by computational analysis, and to show their precise positions relative to known or predicted genes. This allows the identification of TREs most likely to function as promoters or enhancers for neuronal-specific target genes.
Annotation / genetic database analysis
An additional module is used to calculate which TRE clusters are within a given distance of a gene known to be expressed specifically in the nervous system, based on genetic information provided by an online annotation database (FlyBase). These TREs are then selected for further analysis.
This integration of computational pattern matching, graphical visualization and functional genomics analysis using online genetics databases has revealed a network of potential targets and provides a testable model for the next stage of genetic pathway and target gene studies.
