An outline of the experimental strategy used by Mango and colleagues [8,9] to identify regulatory motifs that specify temporal and spatial patterns of gene expression during pharyngeal development. (a) RNA was isolated from worms with mutations in the par-1 or skn-1 genes, which have excess or no pharyngeal cells, respectively. (b) The RNA from the two strains was compared using a whole-genome microarray. (c) Transcripts with high levels of expression in par-1 worms compared with skn-1 worms were selected and sorted into groups according to their temporal  or spatial  pattern of expression. For the temporal groupings the genes were divided into those expressed early or late in pharynx development; for the spatial groupings they were divided into those expressed in the muscles, glands, pharyngeal marginal cells or epithelium, plus those that were expressed in both the muscles and the marginal cells. (d) The promoters of the genes in each group were analyzed using the Improbizer algorithm to find sequence elements that were significantly enriched in each group; these were named Early-1, M2, and so on. A selection of these is shown.
Banerjee and Slack Genome Biology 2005 6:205 doi:10.1186/gb-2005-6-2-205