Table 1

Table 1. Comparison of protein-protein interactions identified by two-hybrid vs. mass spectrometry
ORF	Two-hybrid prediction	Mass spectrometry prediction
YFR003C	Morphogenesis	Cell cycle
YKL088W	Cellular process	Coenzyme A biosynthesis
YML023C	Cell growth and/or maintenance	DNA repair
YDR288W	Response to DNA damage stimulus	DNA repair
YGR002C	Nuclear division	Histone acetylation
YLR424W	Nucleobase, nucleoside, nucleotide and nucleic acid metabolism	mRNA splicing
YDR013W (PSF1)	DNA repair	Unknown complex 1*
YJL072C (PSF2)	Unknown complex 1	Unknown complex 1*

Assignment of GO terms to uncharacterized yeast proteins based on protein-protein interactions observed by two-hybrid or mass spectrometry methods (Hazbun et al., 2003).GO Biological Process terms were determined by using the GO Term Finder available on the Saccharomyces Genome Database website (www.yeastgenome.org). For each protein, the tool was used to find significant shared GO terms among the interacting proteins identified by two-hybrid or mass spectrometry. From the 100 proteins that were analyzed, 8 proteins had sufficient data that allowed the assignment of GO process terms by both methods. The protein-protein interaction overlap between the methods was low but the Biological Process terms generally agreed in that they were related and within the same branch of the ontology network. However, the two-hybrid predictions resulted in generally lower resolution terms because each had to encompass interactions that included proteins in several related biological processes. The asterisk indicates that these proteins were part of unknown complex 1 and could not be assigned a Biological Process term since all the complex members at the time had unknown function.