[
International Worm Meeting,
2003]
Different functional genomics efforts have been initiated in C. elegans, including RNAi phenotype, expression profile, and protein interaction mapping projects. We are developing Web-accessible database tools to facilitate the archival, distribution, navigation, and mining of these data. RNAiDB (www.rnai.org): RNAiDB is a database tool for the archival and analysis of RNAi-based results from large-scale studies. It presents a view of the genome centered around phenotypic analysis, is fully searchable, and provides a user-friendly interface for navigation with links to external database resources. RNAiDB uses the AceDB database engine and is easily integrated with WormBase through its compatible database models. We are extending the functionality of RNAiDB in several ways. To enhance flexibility for mining phenotypic data we are creating tools such as 'PhenoBlast', which ranks genes on the basis of their overall phenotypic similarities (thus providing a function analogous to that of BLAST for sequence searching). We have extended the RNAiDB data models to accommodate one-to-many mappings between RNAi experiments and potentially inhibited target genes based on sequence analyses such as ePCR or BLAST. We have also created a rich set of new data models for phenotypic scoring together with a comprehensive Web-based data entry system that allows users to record phenotypic data directly into the database as they are being scored in a controlled, systematic manner via a series of Web forms linked to the database. InFuGen: We have begun prototyping a second Web tool to facilitate the exploration of different types of functional genomics data in an integrated fashion, which we call "InFuGen" (Integrated Functional Genomics). The idea behind this tool is to provide the ability to visualize and navigate network relationships between genes based on correlations from a combination of different functional and genomic data such as phenotypic signatures, gene expression profiles, protein interaction maps, sequence similarity, domain composition, and functional annotations.