ITR: Development of Novel Computational Methods for Genome-Wide Discovery of Gene Function and Networks

University Of Texas At Austin, Austin TX

Investigators

Abstract

EIA-0219061 Marcotte, Edward M University of Texas ITR: Development of novel computational methods for genome-wide discovery of gene function and networks Of the roughly 40,000 genes encoded by the human genome, as with every other genome sequenced to date, about half are completely uncharacterized and of unknown function. There is a broad need for methods to discover the functions of these thousands of uncharacterized genes, as well as how the gene products participate in networks, pathways and systems in the cell. This project's goal is to develop novel computational methods for discovering the functions of genes on a genome-wide scale, and to discover how the genes are organized into systems and pathways. Several novel methods are proposed capable of providing such information. The essence of these methods, called "non-homology" methods, is that they analyze contextual properties of genes-such as which organisms the genes appear in, which genes can be found fused together, and other properties-in addition to the sequences of the genes. Such contextual properties turn out to provide a tremendous increase in the ability of computational methods to discover gene function and gene networks. At the core of this proposal is a novel graph-based method for associating genes together that operate in the same cellular pathway, essentially resulting in a "functional map" of the genes. This method is combined with a new computational method for finding specific physical interaction partners for proteins in large sequence families, and with methods to visualize the resultant complex gene networks. Application of these methods should improve our understanding of the functions of the thousands of uncharacterized genes in each sequenced genome.