Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets

The integration of multi-omic data using machine learning methods has been focused on solving relevant tasks such as predicting sensitivity to a drug or subtyping patients. Recent integration methods, such as joint Non-negative Matrix Factorization, have allowed researchers to exploit the information in the data to unravel the biological processes of multi-omic datasets.

We present a novel method called Multi-project and Multi-profile joint Non-negative Matrix Factorization capable of integrating data from different sources, such as experimental and observational multi-omic data. The method can generate co-clusters between observations, predict profiles and relate latent variables. We applied the method to integrate low-grade glioma omic profiles from The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia projects. The method allowed us to find gene clusters mainly enriched in cancer-associated terms. We identified groups of patients and cell lines similar to each other by comparing biological processes. We predicted the drug profile for patients, and we identified genetic signatures for resistant and sensitive tumors to a specific drug.

Source code repository is publicly available at https:/bitbucket.org/dsalazarb/mmjnmf/-Zenodo DOI: 10.5281/zenodo.5150920.

Supplementary data are available at Bioinformatics online.