Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm

• Published in: PloS one 2017-05, Vol.12 (5), p.e0176278-e0176278
• Main Authors: Chalise, Prabhakar, Fridley, Brooke L
• Format: Article
• Language: English
• Subjects: Abnormalities; Algorithms; Antibodies; Applications of mathematics; Assaying; Bayesian analysis; Bioinformatics; Biological activity; Biology; Biology and life sciences; Biometrics; Brain cancer; Breast cancer; Breast Neoplasms - classification; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Cancer; Classification; Cluster Analysis; Clusters; Coefficients; Computational Biology - methods; Computer applications; Computer graphics; Computer programs; Computer Simulation; Constraints; Convergence; Data processing; Databases, Genetic; Deoxyribonucleic acid; DNA; DNA Copy Number Variations; DNA methylation; DNA Methylation - physiology; DNA microarrays; Epidermal growth factor receptors; Estimation; Etiology; Factorization; Fruits; Gene expression; Gene Expression - physiology; Genomes; Genomic analysis; Genomics; Glioblastoma; Glioblastoma - classification; Glioblastoma - genetics; Glioblastoma - metabolism; Humans; Intelligence; Jaw; Machine learning; Mathematical models; Matrices (Mathematics); Medicine and Health Sciences; Methods; MicroRNAs - metabolism; Nonlinear programming; Objective function; Ovarian cancer; Ovarian carcinoma; Pharmacology; Physical characteristics; Physical Sciences; Probability distribution; Research and Analysis Methods; RNA, Messenger - metabolism; Simulation; Software; Statistical analysis; Statistical distributions; Tumors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0176278

Integrative analyses of high-throughput 'omic data, such as DNA methylation, DNA copy number alteration, mRNA and protein expression levels, have created unprecedented opportunities to understand the molecular basis of human disease. In particular, integrative analyses have been the cornerstone in the study of cancer to determine molecular subtypes within a given cancer. As malignant tumors with similar morphological characteristics have been shown to exhibit entirely different molecular profiles, there has been significant interest in using multiple 'omic data for the identification of novel molecular subtypes of disease, which could impact treatment decisions. Therefore, we have developed intNMF, an integrative approach for disease subtype classification based on non-negative matrix factorization. The proposed approach carries out integrative clustering of multiple high dimensional molecular data in a single comprehensive analysis utilizing the information across multiple biological levels assessed on the same individual. As intNMF does not assume any distributional form for the data, it has obvious advantages over other model based clustering methods which require specific distributional assumptions. Application of intNMF is illustrated using both simulated and real data from The Cancer Genome Atlas (TCGA).