Category: Biotechnology

Which Gene Influences What? Data Desk® Aids in Gene Mapping

Using Data Desk to help find genetic explanations for differences in brain architecture and predisposition to disease, Rob Williams and his colleagues at the University of Tennessee Health Science Center, analyzes enormous datasets describing very tiny brains. He studies mouse brains in order to suggest something about the genetic sources of brain differences in humans. The brains of any two mice, even two close relatives, can differ dramatically on any number of characteristics. Rob is trying to identify and locate the genes that are associated with the differences and to learn something about the interaction of these genes.

The process Rob's team uses is called "complex trait analysis." Data Desk serves important functions at the beginning and final stages of the process. In the first part of an investigation, says Rob, "We look for key features, say for example, number of photo receptors. We may locate up to 400 of the 'marker' genes and include 1,000 animals in the study. Then to assess the quality of data we've pulled together we do outlier detection and distribution analyses." The team has custom software that uses the combed-out data to create a gene map. Once the genes have been located, the locations in the gene map are used as predictors of certain characteristics of the brain.

At this point, Rob and his colleagues use Data Desk to create a general linear model to test for correlations that demonstrate the influence of specific genes on particular brain characteristics and that suggest the interaction of specific genes as an influence to create this influence.

"What Data Desk is really great for is swimming through large datasets," Rob says. Inspired by this capability, he and colleague Ken Manley, at the Roswell Park Cancer Institute, Buffalo, New York are collaborating with Data Description to plan a set of tools based on Data Desk that can be used by other researchers doing genetic studies. "We'd like to provide the community with the cool features of Data Desk - interactivity, speed, dynamic graphics." The software Data Description and the researchers envision will combine Data Desk technology with such established web resources for neurogenetic research as quantitative trait loci, recombinant inbred data, and established statistics.

Click on the picture above to see a complete screenshot.

Name: Rob Williams

Organization: University of Tennessee Health Science Center

Location: Memphis, Tennessee

Version: Data Desk 6.2, Mac OS X

Typical Dataset: 400 of the 'marker' genes per animal using 1,000 animals

Analysis: "What Data Desk is really great for is swimming through large datasets."

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