GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox

Abstract

High-throughput gene expression analysis has become a frequent and powerful research tool in biology. At present, however, few software applications have been developed for biologists to query large microarray gene expression databases using a Web-browser interface. We present GENEVESTIGATOR, a database and Web-browser data mining interface for Affymetrix GeneChip data. Users can query the database to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs. Reversely, mining tools allow users to identify genes specifically expressed during selected stresses, growth stages, or in particular organs. Using GENEVESTIGATOR, the gene expression profiles of more than 22,000 Arabidopsis genes can be obtained, including those of 10,600 currently uncharacterized genes. The objective of this software application is to direct gene functional discovery and design of new experiments by providing plant biologists with contextual information on the expression of genes. The database and analysis toolbox is available as a community resource at https://www.genevestigator.ethz.ch.

Figure 1.

Concept and design of GENEVESTIGATOR. The experimenter submits RNA profiling data to the database curator, who processes the data and uploads it to the database. The datawarehouse contains raw signal intensity and P values, as well as preprocessed tables. A Webserver application acts as an interface between users and the GENEVESTIGATOR database.

Figure 2.

Screenshots of some of the features of GENEVESTIGATOR. Top left, Logo and available tools. A, Chip Selection tool; B, Digital Northern; C, Gene Correlator; D and E, Gene Atlas (relates to plant anatomy); F and G, Gene Chronologer (relates to the plant growth stages); H and I, Response Viewer (relates to environmental factors); J to L, Meta-Analyzer (multiple gene analysis with respect to anatomy, growth stage, and environmental factors); M and N, Database tool for viewing experiment and array annotation, and Documentation section for user information.

Figure 3.

Validation of the quality of data generated by GENEVESTIGATOR. A to G, Expression of organ or tissue-specific marker genes used for testing the Gene Atlas tool (A, AGL12, At1g71692; B, AGL14, At4g11880; C, AGL17, At2g22630; D, At1g55570; E, At2g25600; F, At1g19150; G, At3g08940). H to K, Expression of growth stage specific marker genes used to validate the Gene Chronologer tool (H, ATEM1, At3g51810; I, At4g37580; J, APETALA1, At1g69120; K, FLOWERING LOCUS T, At1g65480). L to Q, Expression of environmental factor specific marker genes to validate the Response Viewer tool (L, At4g14690; M, At5g54190; N, ERF1, At3g23240; O, AtERF1, At4g17599; P, AtERF2, At5g47220; Q, AtERF13, At2g44840).