Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes

Abstract

The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation.

Figure 1

System architecture of Genevestigator. The white spaces show the possible boundaries between computers. The application server modules are running in a Tomcat web container and communicate with the database through the JDBC protocol. A thick Java applet reads data from an application server and a cache subsystem through a custom RPC protocol tunneled over http/https. A load-balancing subsystem ensures that the clients can communicate with a scalable cluster of application servers. Moreover, the application servers can be transparently configured to work with a database cluster of an arbitrary size.

Figure 2

Data flow and analysis cycle. Schematic overview of Genevestigator V3. (a) Data flow through the Genevestigator system. Microarray experiments are performed by the research community and either stored in public repositories or sent directly to Genevestigator. Data and annotations are curated and quality controlled by Genevestigator curators and stored in the Genevestigator system (see Figure 1). (b) Expression analysis cycle. The user starts at the Genevestigator website, from where the client application is launched. Four toolsets allow different types of analysis. Results obtained are used either to confirm an existing hypothesis or to create new ones that can be validated in the laboratory. Figures from Genevestigator can be exported in a variety of formats. The website provides user support and a community exchange platform.