Genome Biology 2004, 5:227 co m m ent review s repo rts depo sited research interactio ns info rm atio n refereed research 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: [email protected] 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. 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 Tracking developmental changes in gene expression The availability of genome-wide expression analysis tools allows one to investigate the details of transcriptional regula- tion 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 condi- tions resemble each other, pointing out similarities - or dis- similarities - 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 speci- ficity. Previous studies of gene expression during the devel- opment of multicellular organisms have mostly emphasized either the developmental stage or the cell-type aspect.