CORE B: Functional Annotation Core ABSTRACT The ultimate goal of the Program is to develop novel statistical methods to study cancer. One important aspect of it is to understand the biology, or function, underlying the large amount of data that will be analyzed. All four projects in this program will deal with large amount genetic and protein data. Functional annotations to these datasets will be crucial for each project to properly analyze the data and interpret the results. In the current funding period, the Core developed an integrated annotation query system (AnnoQ, www.annoq.org) that incorporates existing external annotation tools and resources, as well as in-house annotation infrastructure, including Peregrine (www.peregrineproj.org), an enhancer to gene link database developed by this core. The system allows researchers to quickly retrieve annotation data through either an interactive user interface or a programmatic API. It is currently in beta release and is being used by many researchers within USC. We will continue to improve the system by focusing on data quality, system performance, and user support. It will be our top priority to keep the annotation data up to date, and to maintain high quality and accuracy of the data. Benchmarking studies will be designed to analyze and evaluate the quality of the data. In additional, query software and packages using the AnnoQ system will be developed and made available through Core C. With anticipated increase in data size and user traffic, hardware upgrade and enhancement of internet security will become essential. Finally, regular meetings with program members will allow us to provide proper training and ensure that the system meets their needs.