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Tracking developmental changes in gene expression

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Published: 27 May 2004 Genome Biology 2004, 5:227 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/6/227 © 2004 BioMed Central Ltd reviews Abstract Separation of cell types and developmental stages in the Arabidopsis root and subsequent expression profiling have yielded a valuable dataset that can be used to select candidate genes for detailed study and to start probing the complexities of gene regulation in plant development. reports deposited research Tracking developmental changes in gene expression The availability of genome-wide expression analysis tools allows one to investigate the details of transcriptional. | Minireview Root genomics towards digital in situ hybridization Ben Scheres Henk van den Toorn and Renze Heidstra Address Department of Molecular Cell Biology Utrecht University Padualaan 3 3584 CH Utrecht The Netherlands. Correspondence Ben Scheres. E-mail b.scheres@bio.uu.nl Published 27 May 2004 Genome Biology 2004 5 227 The electronic version of this article is the complete one and can be found online at http genomebiology.com 2004 5 6 227 2004 BioMed Central Ltd Abstract Separation of cell types and developmental stages in the Arabidopsis root and subsequent expression profiling have yielded a valuable dataset that can be used to select candidate genes for detailed study and to start probing the complexities of gene regulation in plant development. Tracking developmental changes in gene expression The availability of genome-wide expression analysis tools allows one to investigate the details of transcriptional regulation during development. Clustering methods can be used to group genes whose expression varies in a similar way in response to developmental changes. Such clustering methods can reveal two major trends. First they can reveal groups of genes that are co-regulated and therefore suggest which genes function together during a given developmental process. Second clustering methods can reveal which conditions resemble each other pointing out similarities - or dissimilarities - in developmental states that might not be obvious otherwise. Two major developmental parameters for analysis by gene-expression profiling are progression in time developmental stage and tissue region or cell-type specificity. Previous studies of gene expression during the development of multicellular organisms have mostly emphasized either the developmental stage or the cell-type aspect. For example clusters of genes co-expressed during the entire life cycle have been defined in Caenorhabditis elegans 1 and changes at the transition from cell proliferation to cell differentiation .