• normal cells versus diseased cells.
• normal cells versus those responding to a stimulus.
• cells from same organism, at different stages of development (e.g., embryo versus adult).
• normal (historic wildtype) cells versus genetically engineered cells (e.g., those that have been engineered to cure a disease, resist a herbicide, etc.).
• normal cells versus those same cells treated with a given pharmaceutical or nutraceutical (candidate).

Analysis generally involves measurement of gene expression markers (i.e., molecules synthesized, or cellular consequences such as apoptosis) to determine which genes are expressed (and when/how much, etc.). For example, during 2002, Yiwei Li utilized a cDNA-based microarray to show that genistein (an isoflavone obtained from soybeans) down-regulated the expression levels of eleven human genes (which have been shown to be involved in angiogenesis and/or cancer metastasis) and up-regulated (i.e., increased the expression levels of) two human genes associated with connective tissue cell signaling.

Scientists discovered via gene expression analysis that humans of Asian ancestry are more likely to express the particular mutation of the gene for epidermal growth factor receptor that can result in lung cancer.