<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Global studies of protein–protein interactions are crucial to both elucidating gene
function and producing an integrated view of the workings of living cells. High-throughput
studies of the yeast interactome have been performed using both genetic
and biochemical screens. Despite their size, the overlap between these experimental
datasets is very limited. This could be due to each approach sampling only a small
fraction of the total interactome. Alternatively, a large proportion of the data from
these screens may represent false-positive interactions. We have used the Genome
Information Management System (GIMS) to integrate interactome datasets with
transcriptome and protein annotation data and have found significant evidence that
the proportion of false-positive results is high. Not all high-throughput datasets are
similarly contaminated, and the tandem affinity purification (TAP) approach appears
to yield a high proportion of reliable interactions for which corroborating evidence
is available. From our integrative analyses, we have generated a set of verified
interactome data for yeast.</p>
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Comp Funct Genomics. 2004 Jul; 5(5):382-402