Web-based analysis of the mouse transcriptome using Genevestigator.
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.


METHODS
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.


CONCLUSIONS
The Genevestigator-Mouse database effectively provides biologically meaningful results and can be accessed at https://www.genevestigator.ethz.ch.
Laule
Oliver
O
Institute of Plant Sciences, ETH Zurich, 8092 Zurich, Switzerland. ola@ethz.ch
Hirsch-Hoffmann
Matthias
M
Hruz
Tomas
T
Gruissem
Wilhelm
W
Zimmermann
Philip
P
D000818:Animals; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D016247:Information Storage and Retrieval; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015203:Reproducibility of Results; D014158:Transcription, Genetic; D014584:User-Computer Interface