Dynamic networks reveal key players in aging

Motivation: Since susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and their protein products in isolation, ignoring their connectivities. However, proteins function by interacting with other proteins, and this is exactly what biological networks (BNs) model. Thus, analyzing the proteins' BN topologies could contribute to understanding of aging. Current methods for analyzing systems-level BNs deal with their static representations, even though cells are dynamic. For this reason, and because different data types can give complementary biological insights, we integrate current static BNs with aging-related gene expression data to construct dynamic, age-specific BNs. Then, we apply sensitive measures of topology to the dynamic BNs to study cellular changes with age. Results: While global BN topologies do not significantly change with age, local topologies of a number of genes do. We predict such genes as aging-related. We demonstrate credibility of our aging-related predictions by: 1) observing significant overlap between the predictions and "ground truth" aging-related genes; 2) showing that our predictions group by functions and diseases that are different than functions and diseases of genes that we do not predict as aging-related; 3) observing significant overlap between functions and diseases that are enriched in our predictions and those that are enriched in "ground truth" aging-related data; 4) providing evidence that diseases which are enriched in our predictions are linked to human aging; and 5) validating our predictions in the literature. This work was published in arXiv:1307.3388 [cs.CE], 2013.