Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets
Visualitza/Obre
10.1093/bioinformatics/btab579
Inclou dades d'ús des de 2022
Cita com:
hdl:2117/362465
Tipus de documentArticle
Data publicació2021
EditorOxford University Press
Condicions d'accésAccés obert
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Abstract
Abstract
Motivation
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.
Results
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.
CitacióSalazar, D.A.; Przulj, N.; Valencia, C.F. Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets. "Bioinformatics", 2021, vol. 37, núm. 24, p. 4801-4809.
ISSN1367-4803
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