sTPLS: identifying common and specific correlated patterns under multiple biological conditions.

Abstract

The rapidly emerging large-scale data in diverse biological research fields present valuable opportunities to explore the underlying mechanisms of tissue development and disease progression. However, few existing methods can simultaneously capture common and condition-specific association between different types of features across different biological conditions, such as cancer types or cell populations. Therefore, we developed the sparse tensor-based partial least squares (sTPLS) method, which integrates multiple pairs of datasets containing two types of features but derived from different biological conditions. We demonstrated the effectiveness and versatility of sTPLS through simulation study and three biological applications. By integrating the pairwise pharmacogenomic data, sTPLS identified 11 gene-drug comodules with high biological functional relevance specific for seven cancer types and two comodules that shared across multi-type cancers, such as breast, ovarian, and colorectal cancers. When applied to single-cell data, it uncovered nine gene-peak comodules representing transcriptional regulatory relationships specific for five cell types and three comodules shared across similar cell types, such as intermediate and naïve B cells. Furthermore, sTPLS can be directly applied to tensor-structured data, successfully revealing shared and distinct cell communication patterns mediated by the MK signaling pathway in coronavirus disease 2019 patients and healthy controls. These results highlight the effectiveness of sTPLS in identifying biologically meaningful relationships across diverse conditions, making it useful for multi-omics integrative analysis.