Gaussian Embedding for Large-scale Gene Set Analysis.

Gene sets, including protein complexes and signaling pathways, have proliferated greatly, in large part as a result of high-throughput biological data. Leveraging gene sets to gain insight into biological discovery requires computational methods for converting them into a useful form for available machine learning models. Here, we study the problem of embedding gene sets as compact features that are compatible with available machine learning codes. We present Set2Gaussian, a novel network-based gene set embedding approach, which represents each gene set as a multivariate Gaussian distribution rather than a single point in the low-dimensional space, according to the proximity of these genes in a protein-protein interaction network. We demonstrate that Set2Gaussian improves gene set member identification, accurately stratifies tumors, and finds concise gene sets for gene set enrichment analysis. We further show how Set2Gaussian allows us to identify a previously unknown clinical prognostic and predictive subnetwork around NEFM in sarcoma, which we validate in independent cohorts.

Insulin resistance contributes to aberrant stress responses in the Tg2576 mouse model of Alzheimer's disease.

We previously reported aberrant stress responses and impaired glucose tolerance in transgenic Tg2576 mice, a model of Alzheimer's disease (AD). Here we report that by 8 months of age, Tg2576 mice had lower basal serum insulin concentrations and exhibited a delayed insulin-induced reduction in blood glucose levels relative to wild-type mice. However, the basal levels of blood glucose and percent glycosylated hemoglobin (%HbA1c) were similar between the two groups of mice. While the basal levels of serum corticosterone were similar between Tg2576 and wild-type mice, an overnight fasting caused a greater rise in serum corticosterone levels and an excessive reduction in serum insulin concentrations in the transgenics. At 9 months of age, we began administering Tg2576 mice rosiglitazone, an agonist of peroxisome proliferator-activated receptor-gamma that increases peripheral insulin sensitivity, and after 6 weeks of administration the Tg2576 mice had the same response to insulin and increase in serum corticosterone levels after an overnight fast as did wild-type mice. By 13 months of age, untreated Tg2576 mice had become hyperinsulinemic, in contrast to Tg2576 mice administered rosiglitazone for 4 months where the serum insulin concentrations were maintained at levels observed in wild-type mice. These results provide evidence for a relationship between insulin resistance, impaired regulation of insulin and glucose levels, and aberrant stress responses in Tg2576 mice.