Genome-wide search algorithms for identifying dynamic gene co-expression via Bayesian variable selection.
Stat Med
; 42(30): 5616-5629, 2023 12 30.
Article
em En
| MEDLINE
| ID: mdl-37806971
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Genômica
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Stat Med
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
Estados Unidos