PMID- 35144027 OWN - NLM STAT- MEDLINE VI - 49 IP - 9 TI - Highly Regional Genes: graph-based gene selection for single-cell RNA-seq data. PG - 891-899 CI - Copyright © 2022 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - China TA - J Genet Genomics JT - Journal of genetics and genomics = Yi chuan xue bao JID - 101304616 IS - 1673-8527 (Print) LID - S1673-8527(22)00033-9 [pii] LID - 10.1016/j.jgg.2022.01.004 [doi] FAU - Wu, Yanhong AU - Wu Y AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Hu, Qifan AU - Hu Q AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Wang, Shicheng AU - Wang S AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Liu, Changyi AU - Liu C AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Shan, Yiran AU - Shan Y AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Guo, Wenbo AU - Guo W AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Jiang, Rui AU - Jiang R AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Wang, Xiaowo AU - Wang X AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. FAU - Gu, Jin AU - Gu J AD - MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China. Electronic address: jgu@tsinghua.edu.cn. IS - 1673-8527 (Linking) SB - IM MH - Algorithms MH - Cluster Analysis MH - Gene Expression Profiling/methods MH - Humans MH - RNA-Seq MH - Sequence Analysis, RNA/methods MH - *Single-Cell Analysis/methods MH - *Transcriptome/genetics OTO - NOTNLM OT - Feature selection OT - Graphical models OT - Regional patterns OT - Single-cell RNA-sequencing OT - Spatially resolved transcriptomic data DCOM- 20220926 LR - 20221021 DP - 202209 DEP - 20220208 AB - Gene selection is an indispensable step for analyzing noisy and high-dimensional single-cell RNA-seq (scRNA-seq) data. Compared with the commonly used variance-based methods, by mimicking the human maker selection in the 2D visualization of cells, a new feature selection method called HRG (Highly Regional Genes) is proposed to find the informative genes, which show regional expression patterns in the cell-cell similarity network. We mathematically find the optimal expression patterns that can maximize the proposed scoring function. In comparison with several unsupervised methods, HRG shows high accuracy and robustness, and can increase the performance of downstream cell clustering and gene correlation analysis. Also, it is applicable for selecting informative genes of sequencing-based spatial transcriptomic data.