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The needle in the haystack: identifying gene function

To answer big questions in science, sometimes you have to go big. More than a decade ago, the human genome was sequenced in its entirety. To gain perspective on how big a question the sequence of our genome was, consider this: If you lined up human DNA, it could reach the sun and back… six times!

Knowing the sequence of genes isn’t everything though, and approximately one-third of our genome (or about 6,000 genes) has unknown or poorly characterized function.

Researchers at Stanford, led by Tobias Meyer, PhD, professor of cell biology, and graduate student Gautam Dey developed a comparative search engine to help identify the function for a small group of genes. The study was published online Feb. 12 in Cell Reports, and the search engine is accessible here.

“After the human genome was sequenced, scientists thought it would be a very short time before we knew what all the genes are doing,” Meyer told me. “It turned out not to be so easy, and we are currently in a holding pattern before we can really make use of all the genomic information.”

Having a starting point for identifying a gene’s function is important. Otherwise, it can be like searching for a needle in a haystack, as I wrote in a story on the paper:

To computationally identify the function of a gene, scientists have a few options. The easiest is finding another human gene with a similar sequence for comparison. Another option is searching for human genes with shared ancestry for comparison. But sometimes there is no human gene available for comparison, and scientists have to compare human genes to those from other species.

The search engine relies on accessing genomic sequences from humans and other species that are contained in the RefSeq online database and then narrows the myriad of possible starting points for identifying human gene function. This study is an example of using freely available big datasets to make it easy for scientists to ask and answer difficult questions, which is a current trend spanning the biological sciences.

Kimberlee D’Ardenne is a writing intern in the medical school’s Office of Communication and Public Affairs.

Previously: Open source encyclopedia of human genome’s functional elements in the works, Of mice and men: Stanford researchers compare mammal’s genomes to aid human clinical research and DNA origami: How our genomes fold


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