Learning Coexpression Networks from Single Cell Gene Expression

Andrew McDavid, Assistant Professor, Dept. of Biostatistics and Computational Biology, University of Rochester

Friday, April 12, 2019 - 3:30pm

Bulk gene expression experiments relied on aggregations of thousands of cells to measure the average expression in an organism. Advances in microfluidic and droplet sequencing now permit expression profiling in single cells. This study of cell-to-cell variation reveals that individual cells lack detectable expression of transcripts that appear abundant on a population level, giving rise to zero-inflated expression patterns. To infer gene co-regulatory networks from such data, we propose a multivariate Hurdle model. It is comprised of a mixture of singular Gaussian distributions. We employ neighborhood selection with the pseudo-likelihood and a group lasso penalty to select and fit undirected graphical models that capture conditional independences between genes. The proposed method is more sensitive than existing approaches in simulations, even under departures from our Hurdle model.  It infers network structure not revealed by other methods; or in bulk data sets.

Seminars generally take place in 116 Old Chemistry Building on Fridays from 3:30 - 4:30 pm. For additional information contact: karen.whitesell@duke.edu or phone 919-684-8029. Sorry, but we do not have reprints available. Please feel free to contact the authors by email for follow-up information, articles, etc. Reception following seminar in 203B Old Chemistry.

Old Chemistry 116

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