title: Tools for managing and analyzing microarray data.
abstract: The microarray-based analysis of gene expression has become a workhorse for biomedical research. Managing the amount and diversity of data that such experiments produce is a task that must be supported by appropriate software tools, which led to the creation of literally hundreds of systems. In consequence, choosing the right tool for a given project is difficult even for the expert. We report on the results of a survey encompassing 78 of such tools, of which 22 were inspected in detail and seven were tested hands-on. We report on our experiences with a focus on completeness of functionality, ease-of-use, and necessary effort for installation and maintenance. Thereby, our survey provides a valuable guideline for any project considering the use of a microarray data management system. It reveals which tasks are covered by mature tools and also shows that important requirements, especially in the area of integrated analysis of different experimental data, are not yet met satisfyingly by existing systems.
authors.affiliation: Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, 12489 Berlin, Germany. koschmie@informatik.hu-berlin.de
authors.forename: André
authors.initials: A
authors.lastname: Koschmieder
authors.forename: Karin
authors.initials: K
authors.lastname: Zimmermann
authors.forename: Silke
authors.initials: S
authors.lastname: Trissl
authors.forename: Thomas
authors.initials: T
authors.lastname: Stoltmann
authors.forename: Ulf
authors.initials: U
authors.lastname: Leser
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D039781:PubMed; D012984:Software