Robust kernel canonical correlation analysis to detect gene-gene co-associations: A case study in genetics

Abstract

The kernel canonical correlation analysis based U-statistic (KCCU) is being used to detect nonlinear gene–gene co-associations. Estimating the variance of the KCCU is however computationally intensive. In addition, the kernel canonical correlation analysis (kernel CCA) is not robust to contaminated data. Using a robust kernel mean element and a robust kernel (cross)-covariance operator potentially enables the use of a robust kernel CCA, which is studied in this paper. We first propose an influence function-based estimator for the variance of the KCCU. We then present a non-parametric robust KCCU, which is designed for dealing with contaminated data. The robust KCCU is less sensitive to noise than KCCU. We investigate the proposed method using both synthesized and real data from the Mind Clinical Imaging Consortium (MCIC). We show through simulation studies that the power of the proposed methods is a monotonically increasing function of sample size, and the robust test statistics bring incremental gains in power. To demonstrate the advantage of the robust kernel CCA, we study MCIC data among 22,442 candidate Schizophrenia genes for gene–gene co-associations. We select 768 genes with strong evidence for shedding light on gene–gene interaction networks for Schizophrenia. By performing gene ontology enrichment analysis, pathway analysis, gene–gene network and other studies, the proposed robust methods can find undiscovered genes in addition to significant gene pairs, and demonstrate superior performance over several of current approaches.