Elucidating the Genetic Networks of Development: A Bioinformatics Approach

Bioinformatics traditionally covers data on protein structures, DNA sequences and gene mapping, but, especially since the initiation of the Human Genome Mapping Project, it now includes functional and other information. Here, we consider how bioinformatics can also handle patterns of gene expression in embryos, particularly the mouse, and discuss how the use of databases containing such information could help solve one of the major problems in contemporary developmental biology, elucidating the genetic networks responsible for tissue differentiation and organogenesis.

The key data here are the expression patterns of genes and the phenotypic effects of gene mutations; once these are in place for a given phenomenon, we can start to identify the underlying genetic network. Unfortunately, this information cannot usually be obtained from the standard literature databases, even with their search facilities: Not only are the relevant terms often absent from titles and abstracts, but the data are sometimes not published, as researchers now have more material than editors will accept. The most important point, however, is that the gene-expression descriptions are not made with a standardized nomenclature or other spatial reference so that one cannot be sure whether literature searches based on a gene or a tissue name are comprehensive. Those who work with gene expression are discovering something that has been obvious for some time to people in other fields: The best way of archiving and accessing data is through databases.