Functional Genomics Annotation: It's Logical!

© 2004 AAAS

Researchers are now using symbolic logic as a proteomics tool. Todd Yeates and colleagues at the University of California, Los Angeles, used logic analysis of phylogenetic profiles to identify functional correlations between proteins.¹ These correlations can be used to make inferences about the likely functions of many previously uncharacterized genes and proteins, Yeates says.

Yeates' team identified eight different logic statements representing all the possible relationships between three proteins. For example, protein C is present if and only if protein A and protein B are both present; or, protein C is present if and only if protein A is present and protein B is absent. Using such statements, the group examined the complete set of proteins, divided into 4,873 families known as clusters of orthologous groups, from the fully sequenced and publicly available genomes of 67 organisms, mostly bacteria and archaea.

The team found 750,000...