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Robust graph regularized sparse orthogonal nonnegative matrix factorization for identifying differentially expressed genes

With the advent of sequencing technology, numerous gene expression data are generated. Identifying differentially expressed genes play an important role in the gene therapy of cancer patients. As an useful mathematical tool, nonnegative matrix factorization (NMF) has been successfully used for identifying differentially expressed genes. In this paper, a novel method named robust graph regularized sparse orthogonal nonnegative matrix factorization (RGSON) is proposed and used for identifying differentially expressed genes, which introduces manifold learning, L1 and orthogonal constraints into the objective function. In particular, L2,1-norm minimization is enforced on the objective function to improve the robustness of the algorithm. To prove the validity of the algorithm, experiments on the real genomic dataset are conducted. The results show that RGSON performs more effective than many other methods for identifying differentially expressed genes.