Stanford researcher finds method to define genetic 'words'

STANFORD, Calif. - With the human genome in hand, scientists now know the roughly 30,000 words making up the language of the human body. But what do those words mean? Stuart Kim, PhD, associate professor of developmental biology and genetics at the Stanford School of Medicine, has created the first dictionary that defines them.

His work, published in the Aug. 21 advance online version of the journal Science, could help researchers understand the role of newly identified genes. It also provides a glimpse into how a gene's function has evolved over time. "This tool tells you which genetic words are used together. If I see a new word and I see its context, I know what that word means," Kim said.

Kim's method works because scientists already understand the role many proteins play within a cell. Of these known genes, those involved in the same process, such as cell division, all tend to be active at the same time. Relying upon context, scientists can deduce that an undefined gene active at the same time as genes with a known function is probably involved in the same process.

Kim and graduate student Joshua Stuart created their genetic dictionary from gene activity data in four organisms: humans, fruit flies, a roundworm called C. elegans and yeast. Previous experiments at Stanford have yielded a wealth of information about when and in what tissues the genes in these organisms become active.

From these data, Kim and his colleagues figured out which genes happened to be churning out protein at the same time. Their results showed groups of genes with identical patterns of activity. Some genes within these groups have known activities, providing a context for the many genes whose function was previously unknown.

Kim and his colleagues tested their resource using five genes with previously unknown functions. These genes were always active at the same time as a network of genes known to be involved in cell proliferation. These genes also

Contact: Amy Adams
Stanford University Medical Center

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