Analyzing the expression levels of different genes in different cells or conditions provides researchers with a rough functional analysis of genomic sequence information and a selection of potential drug targets. Molecular array technology and gene chips have enabled such high-throughput expression analysis, and have reached the point where, for the first time, the entire genome of a eukaryotic organism can be assayed on a single chip.

Besides gene expression analysis, which compares the expression pattern of a large number of genes in different tissues or disease states, array technology also can be used as a diagnostic, for example to identify which mutations are present in a particular gene isolated from a patient or pathogen.