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

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  • Prabhakar Chalise
  • Brooke L Fridley

Abstract

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).

Suggested Citation

  • Prabhakar Chalise & Brooke L Fridley, 2017. "Integrative clustering of multi-level ‘omic data based on non-negative matrix factorization algorithm," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-18, May.
  • Handle: RePEc:plo:pone00:0176278
    DOI: 10.1371/journal.pone.0176278
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    References listed on IDEAS

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    1. Daniel D. Lee & H. Sebastian Seung, 1999. "Learning the parts of objects by non-negative matrix factorization," Nature, Nature, vol. 401(6755), pages 788-791, October.
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    1. Geert-Jan Huizing & Ina Maria Deutschmann & Gabriel Peyré & Laura Cantini, 2023. "Paired single-cell multi-omics data integration with Mowgli," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Mohammadamin Edrisi & Xiru Huang & Huw A. Ogilvie & Luay Nakhleh, 2023. "Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Flavia Esposito, 2021. "A Review on Initialization Methods for Nonnegative Matrix Factorization: Towards Omics Data Experiments," Mathematics, MDPI, vol. 9(9), pages 1-17, April.

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