PUBLICATION

Web-based analysis of the mouse transcriptome using GENEVESTIGATOR^®

Oliver Laule, Matthias Hirsch-Hoffmann, Tomas Hruz, Wilhelm Gruissem and Philip Zimmermann

BMC Bioinformatics 2006, 7:311

Abstract

BACKGROUND: Gene function analysis often requires a complex and laborious sequence of laboratory and computer-based experiments. Choosing an effective experimental design generally results from hypotheses derived from prior knowledge or experimentation. Knowledge obtained from meta-analyzing compendia of expression data with annotation libraries can provide significant clues in understanding gene and network function, resulting in better hypotheses that can be tested in the laboratory.
RESULTS: GENEVESTIGATOR^® is a microarray database and analysis system allowing context-driven queries. Simple but powerful tools allow biologists with little computational background to retrieve information about when, where and how genes are expressed. We manually curated and quality- controlled 3110 mouse Affymetrix arrays from public repositories. Data queries can be run against an annotation library comprising 160 anatomy categories, 12 developmental stage groups, 80 stimuli, and 182 genetic backgrounds or modifications. The quality of results obtained through GENEVESTIGATOR^® is illustrated by a number of biological scenarios that are substantiated by other types of experimentation in the literature.
CONCLUSION: The GENEVESTIGATOR^®-Mouse database effectively provides biologically meaningful results and can be accessed at https://www.genevestigator.ethz.ch.