TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA


Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data

Patrick P.C.W. Kemmeren1, Nynke L. van Berkum1, Jaak Vilo2, Theo Bijma1, Rogier Donders3, Alvis Brazma2 & Frank C.P. Holstege1, 1Genomics Laboratory, Department of Physiological Chemistry and Department of Medical Genetics, University Medical Center Utrecht, THE NETHERLANDS, 2Microarray Informatics group, EMBL-EBI, Hinxton, ENGLAND, 3Centre for Biostatistics, University Utrecht, THE NETHERLANDS

Whole genome sequences and assays capable of determining the properties of thousands of genes in parallel present challenges with regard to accurate data-processing and functional annotation. Here, large collections of DNA microarray expression data are used to verify high-throughput protein interactions and provide functional annotation. This is done by determining which interacting pairs also exhibit mRNA coexpression. Several strategies for determining coexpression are assessed and the results indicate that more than half of all the genuine interactions contained within the high-throughput data sets can be verified in this way. Confidence in 973 out of 5342 recently reported putative S. cerevisiae interactions is increased. Tenative function is assigned to over 300 previously uncharacterized genes. The robustness of these approaches are demonstrated by experiments that test the in silico predictions made. The study shows how the utility of different types of data can be improved, and how well their combination can contribute to functional annotation.

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