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Open AccessArticle

Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles

1
Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
2
Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(8), 611; https://doi.org/10.3390/genes10080611
Received: 21 June 2019 / Revised: 30 July 2019 / Accepted: 7 August 2019 / Published: 13 August 2019
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Abstract

Rapid advance in single-cell RNA sequencing (scRNA-seq) allows measurement of the expression of genes at single-cell resolution in complex disease or tissue. While many methods have been developed to detect cell clusters from the scRNA-seq data, this task currently remains a main challenge. We proposed a multi-objective optimization-based fuzzy clustering approach for detecting cell clusters from scRNA-seq data. First, we conducted initial filtering and SCnorm normalization. We considered various case studies by selecting different cluster numbers ( c l = 2 to a user-defined number), and applied fuzzy c-means clustering algorithm individually. From each case, we evaluated the scores of four cluster validity index measures, Partition Entropy ( P E ), Partition Coefficient ( P C ), Modified Partition Coefficient ( M P C ), and Fuzzy Silhouette Index ( F S I ). Next, we set the first measure as minimization objective (↓) and the remaining three as maximization objectives (↑), and then applied a multi-objective decision-making technique, TOPSIS, to identify the best optimal solution. The best optimal solution (case study) that had the highest TOPSIS score was selected as the final optimal clustering. Finally, we obtained differentially expressed genes (DEGs) using Limma through the comparison of expression of the samples between each resultant cluster and the remaining clusters. We applied our approach to a scRNA-seq dataset for the rare intestinal cell type in mice [GEO ID: GSE62270, 23,630 features (genes) and 288 cells]. The optimal cluster result (TOPSIS optimal score= 0.858) comprised two clusters, one with 115 cells and the other 91 cells. The evaluated scores of the four cluster validity indices, F S I , P E , P C , and M P C for the optimized fuzzy clustering were 0.482, 0.578, 0.607, and 0.215, respectively. The Limma analysis identified 1240 DEGs (cluster 1 vs. cluster 2). The top ten gene markers were Rps21, Slc5a1, Crip1, Rpl15, Rpl3, Rpl27a, Khk, Rps3a1, Aldob and Rps17. In this list, Khk (encoding ketohexokinase) is a novel marker for the rare intestinal cell type. In summary, this method is useful to detect cell clusters from scRNA-seq data. View Full-Text
Keywords: cluster validity indices; fuzzy clustering; Limma; multi-objective optimization; single cell sequencing; TOPSIS cluster validity indices; fuzzy clustering; Limma; multi-objective optimization; single cell sequencing; TOPSIS
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Mallik, S.; Zhao, Z. Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles. Genes 2019, 10, 611.

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