Testing high-dimensional covariance matrices, with application to detecting schizophrenia risk genes. (English) Zbl 1380.62262

Zhu, Lingxue; Lei, Jing; Devlin, Bernie; Roeder, Kathryn

Ann. Appl. Stat. 11, No. 3, 1810-1831 (2017).

Summary: Scientists routinely compare gene expression levels in cases versus controls in part to determine genes associated with a disease. Similarly, detecting case-control differences in co-expression among genes can be critical to understanding complex human diseases; however, statistical methods have been limited by the high-dimensional nature of this problem. In this paper, we construct a sparse-Leading-Eigenvalue-Driven (sLED) test for comparing two high-dimensional covariance matrices. By focusing on the spectrum of the differential matrix, sLED provides a novel perspective that accommodates what we assume to be common, namely sparse and weak signals in gene expression data, and it is closely related with sparse principal component analysis. We prove that sLED achieves full power asymptotically under mild assumptions, and simulation studies verify that it outperforms other existing procedures under many biologically plausible scenarios. Applying sLED to the largest gene-expression dataset obtained from post-mortem brain tissue from Schizophrenia patients and controls, we provide a novel list of genes implicated in Schizophrenia and reveal intriguing patterns in gene co-expression change for Schizophrenia subjects. We also illustrate that sLED can be generalized to compare other gene-gene “relationship” matrices that are of practical interest, such as the weighted adjacency matrices.

MSC:

62P10	Applications of statistics to biology and medical sciences; meta analysis
62J10	Analysis of variance and covariance (ANOVA)
62H25	Factor analysis and principal components; correspondence analysis
92D20	Protein sequences, DNA sequences

Keywords:

permutation test; high-dimensional data; covariance matrix; sparse principal component analysis