title: Challenges in plant cellular pathway reconstruction based on gene expression profiling.
abstract: Microarrays are used to profile transcriptional activity, providing global cell biology insight. Particularly for plants, interpretation of transcriptional profiles is challenging because many genes have unknown functions. Furthermore, many plant gene sequences do not have clear homologs in other model organisms. Fortunately, over the past five years, various tools that assist plant scientists have been developed. Here, we evaluate the currently available in silico tools for reconstruction of cellular (metabolic, biochemical and signal transduction) pathways based on plant gene expression datasets. Furthermore, we show how expression-profile comparison at the level of these various cellular pathways contributes to the postulation of novel hypotheses which, after experimental verification, can provide further insight into decisive elements that have roles in cellular processes.
authors.affiliation: Nijmegen Centre for Molecular Life Sciences, UMC Radboud University, Geert Grooteplein 26-28, 6525 GA Nijmegen, the Netherlands.
authors.forename: Peter
authors.initials: P
authors.lastname: van Baarlen
authors.forename: H Peter
authors.initials: HP
authors.lastname: van Esse
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
authors.forename: Bart P H J
authors.initials: BP
authors.lastname: Thomma
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D046228:Microarray Analysis; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D015398:Signal Transduction / Q000235:genetics