A. Progress made, including achievements and significance of findings/developments.

The primary focus of the Gerstein lab proteomics work is the correlation of experimental mRNA expression levels with protein abundance. Our stated goals for this reporting period included developing reference human mRNA expression and protein abundance datasets.

The bulk of our development efforts have focused on yeast, as the system for which the most experimental data is currently available.

Additionally, we have considered structural interactions between yeast proteins using a consensus yeast interaction network of 873 proteins which have a total of 1269 interactions. We demonstrated that proteins in the network that can be connected at the same time (i.e., that do not dock at mutually exclusive sites) are more likely to be coexpressed. Additionally, protein network hubs that have multiple interfaces are more likely to be coexpressed with network partners than proteins that have a single interface.

We have also continued development of our proteomics web tools. PARE (Protein Abundance and mRNA Expression Correlation Tool, http://proteomics.gersteinlab.org) provides an automated comparison of mRNA expression levels with protein abundance measurements. The user can choose to correlate all data within the selected pair of datasets, or correlate a focused subset of the data [(MIPS defined complexes and GO categories (according to biological process, molecular function, or cellular component)].

E. Manuscripts (published, submitted, or drafts) derived from
research under the contract

P. M. Kim, L. J. Lu, Y. Xia, and M. Gerstein, âœRelating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insightsâ, Science (2006) 314: 1938.

E. Yu, A. E. C. Burba, and M. Gerstein, âœComparing Protein Abundance and mRNA Expression Dataâ, submitted to BMC Bioinformatics.