Understanding the yeast proteome: a bioinformatics perspective

Rapid development of genomic and proteomic methodologies has provided a wealth of data for deciphering the biomolecular circuitry of a living cell. The main areas of computational research of proteomes outlined in this review are: understanding the system, its features and parameters to help plan the experiments; data integration, to help produce more reliable data sets; visualization and other forms of data representation to simplify interpretation; modeling of the functional regulation; and systems biology. With false-positive rates reaching 50% even in the more reliable data sets, handling the experimental error remains one of the most challenging tasks. Integrative approaches, incorporating results of various genome- and proteome-wide experiments, allow for minimizing the error and bring with them significant predictive power.