Matrix factorization-based data fusion for the prediction of RNA-binding proteins and alternative splicing event associations during epithelial–mesenchymal transition

Abstract

Abstract Motivation The epithelial-mesenchymal transition (EMT) is a cellular–developmental process activated during tumor metastasis. Transcriptional regulatory networks controlling EMT are well studied; however, alternative RNA splicing also plays a critical regulatory role during this process. Unfortunately, a comprehensive understanding of alternative splicing (AS) and the RNA-binding proteins (RBPs) that regulate it during EMT remains largely unknown. Therefore, a great need exists to develop effective computational methods for predicting associations of RBPs and AS events. Dramatically increasing data sources that have direct and indirect information associated with RBPs and AS events have provided an ideal platform for inferring these associations. Results In this study, we propose a novel method for RBP–AS target prediction based on weighted data fusion with sparse matrix tri-factorization (WDFSMF in short) that simultaneously decomposes heterogeneous data source matrices into low-rank matrices to reveal hidden associations. WDFSMF can select and integrate data sources by assigning different weights to those sources, and these weights can be assigned automatically. In addition, WDFSMF can identify significant RBP complexes regulating AS events and eliminate noise and outliers from the data. Our proposed method achieves an area under the receiver operating characteristic curve (AUC) of $90.78\%$, which shows that WDFSMF can effectively predict RBP–AS event associations with higher accuracy compared with previous methods. Furthermore, this study identifies significant RBPs as complexes for AS events during EMT and provides solid ground for further investigation into RNA regulation during EMT and metastasis. WDFSMF is a general data fusion framework, and as such it can also be adapted to predict associations between other biological entities.