Congratulations to Nadia Penrod, a PEMM student who was one of four winners of the Graduate Poster Session held recently at the Top of the Hop! Enjoy your winnings, Nadia! (Read on for a summary of Penrod’s poster.)
Biological function arises from the interactions between the component parts of a cell. We study the interactions between genes in breast tumors and are specifically interested in how these interactions change when the cells are perturbed by a drug. To do this we create gene coexpression networks.
The data underlying our networks come from breast tumor biopsies taken from women during a course of treatment with the drug letrozole. These samples are purified and a gene chip is used to quantify the expression levels of 20,000+ genes per tumor sample. Using the expression level for each gene we can apply a correlation statistic to determine if there is an expression relationship between each pair of genes. We use these correlations to generate a global coexpression network where genes are assigned to nodes and links represent significant correlations between the expression levels of the genes they connect.
By generating a network for each of three time-points we are able to see how the links between genes are rewired in the presence of the drug over time. We identify genes that hold prominent positions within each network, for example, genes that have many links and lie in well-traveled paths. We find that the genes holding these positions are specific to each time point revealing changes in the biological processes that occur as the cells try to mitigate the effects of the drug perturbation.
summary by Nadia Penrod