Dr. J. Michael Cherry

Our largest area of research is the study of the yeast genome by applying bioinformatic techniques. The Saccharomyces Genome Database (SGD) is the result of this effort. This NIH National Resource, a public Web site, provides information on yeast genes, their products and their interactions. My group is expanding SGD to capture the wealth of information from functional genomics, the systematic study of the processes that occur within an organism. The genomic sequence, functional genomic and published literature information are combined in a unique manner that allow the biologist to browse this encyclopedic database. SGD allows four primary methods of entry for browsing. This organization allows users to select a gene knowing its name, map position, DNA or protein sequence, or its role within the cell. In addition, several computational tools are provided to allow the users to explore the collected data sets. SGD has become a tool used daily by thousands of researchers around the globe.

Comparative genomics, the comparison of an organism's DNA sequence or set of predicted protein sequences, is important for elucidating evolutionary relationships. We previously determined a set of ~2000 core proteins within eukaryotes. This set comprises 12% of predicted proteins of the nematode Caenorhabditis and 27% of those predicted for Saccharomyces. We have also shown that this core set is likely present in Drosophila, however a more detailed analysis is planned for the near future. These findings suggest that all eukaryotes contain this set of core eukaryotic functions. Another interesting finding is that within an organism a large percentage it's genes are specific to that organism. As more sequences of eukaryotic genomes are determined we will explore the common and specific sets of proteins they encode.

The third area of research is in the creation of ontologies to aid communication between biologists and genomic databases. We are founding members of the Gene Ontology Collaboration (GO). The GO project, originally conceived by Dr. Michael Ashburner at the University of Cambridge, is a collaboration between five genome databases: FlyBase (Drosophila), Mouse Genome Informatics (Mus), The Arabidopsis Information Resource (Arabidopsis), WormDB (Caenorhabditis) and SGD (Saccharomyces). There are many hierarchical classification systems for protein function, protein secondary structure and protein families. These classifications are very useful, however they were not designed to describe the higher level biological roles gene product's play within the cell. The GO collaboration is developing three independent ontologies that can be used for gene product annotation (www.GeneOntology.org). The three ontologies are Biological Process, Molecular Function and Cellular Component. These ontologies describe a controlled vocabulary that will be significant in the unification of biological terms. The GO terms are used to annotate all yeast genes that have phenotype or functional information from the published literature. The ontologies will allow specific linkage between the member databases of the collaboration. As part of the collaboration we are developing the terms, databases and software.