Document Type
Article
Abstract
A wealth of gene expression data generated by high-throughput techniques provides exciting opportunities for studying gene-gene interactions systematically. Gene-gene interactions in a biological system are tightly regulated and are often highly dynamic. The interactions can change flexibly under various internal cellular signals or external stimuli. Previous studies have developed statistical methods to examine these dynamic changes in gene-gene interactions. However, due to the massive number of possible gene combinations that need to be considered in a typical genomic dataset, intensive computation is a common challenge for exploring gene-gene interactions. On the other hand, oftentimes only a small proportion of gene combinations exhibit dynamic co-expression changes. To solve this problem, we propose Bayesian variable selection approaches based on spike-and-slab priors. The proposed algorithms reduce the computational intensity by focusing on identifying subsets of promising gene combinations in the search space. We also adopt a Bayesian multiple hypothesis testing procedure to identify strong dynamic gene co-expression changes. Simulation studies are performed to compare the proposed approaches with existing exhaustive search heuristics. We demonstrate the implementation of our proposed approach to study the association between gene co-expression patterns and overall survival using the RNA-sequencing dataset from The Cancer Genome Atlas breast cancer BRCA-US project.
Digital Object Identifier (DOI)
Publication Info
Published in Statistics in Medicine, Volume 42, Issue 30, 2023, pages 5616-5629.
Rights
© 2023 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium,provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
APA Citation
Zhang, W., Ma, Z., Wang, L., Fan, D., & Ho, Y. (2023). Genome‐wide search algorithms for identifying dynamic gene co‐expression via Bayesian variable selection. Statistics in Medicine, 42(30), 5616–5629.https://doi.org/10.1002/sim.9928