Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning

In a large-scale gene expression screen 1765 randomly picked cDNAs were ana lyzed by whole-mount in situ hybridization in Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 2 04 of which are novel in Xenopus. Partial DNA sequences and expression patt erns were documented and assembled into a database, 'AXelDB'. Approximately 30% of cDNAs analyzed represent differentially expressed genes and about 5 % show highly regionalized expression. Novel marker genes and potential dev elopmental regulators were found. Differential expression of mitochondrial genes was observed. Marker genes were used to study regionalization of the entire gastrula as well as the tail forming region and the epidermis of the tailbud embryo. Four 'synexpression' groups representing genes with shared , complex expression pattern that predict molecular pathways involved in pa tterning and differentiation were identified. According to their probable f unctional significance these groups are designated as Delta1, Bmp4, ER-impo rt and Chromatin group. Within synexpression groups, a likely function of g enes without sequence similarity can be predicted. The results indicate tha t synexpression groups have strong prognostic value. A cluster analysis was made by comparing gene expression patterns to derive a novel parameter, 't issue relatedness'. In conclusion, this study describes a semi-functional a pproach to investigate genes expressed during early development and provide s global insight into embryonic patterning. (C) 1998 Elsevier Science Irela nd Ltd. All rights reserved.