Single cell clustering based on cell-pair differentiability correlation and variance analysis | |
Jiang, Hao1; Sohn, Lydia L.2; Huan, Haiyan3; Chen, Luonan4,5 | |
刊名 | BIOINFORMATICS |
2018 | |
卷号 | 34期号:21页码:3684-3694 |
关键词 | Embryonic Stem-cells Rna-seq Microenvironment Challenges Genes |
ISSN号 | 1367-4803 |
DOI | 10.1093/bioinformatics/bty390 |
文献子类 | Article |
英文摘要 | Motivation: The rapid advancement of single cell technologies has shed new light on the complex mechanisms of cellular heterogeneity. Identification of intercellular transcriptomic heterogeneity is one of the most critical tasks in single-cell RNA-sequencing studies. Results: We propose a new cell similarity measure based on cell-pair differentiability correlation, which is derived from gene differential pattern among all cell pairs. Through plugging into the frame-work of hierarchical clustering with this new measure, we further develop a variance analysis based clustering algorithm 'Corr' that can determine cluster number automatically and identify cell types accurately. The robustness and superiority of the proposed algorithm are compared with representative algorithms: shared nearest neighbor (SNN)-Cliq and several other state-of-the-art clustering methods, on many benchmark or real single cell RNA-sequencing datasets in terms of both internal criteria (clustering number and accuracy) and external criteria (purity, adjusted rand index, F1-measure). Moreover, differentiability vector with our new measure provides a new means in identifying potential biomarkers from cancer related single cell datasets even with strong noise. Prognosis analyses from independent datasets of cancers confirmed the effectiveness of our 'Corr' method. |
电子版国际标准刊号 | 1460-2059 |
WOS研究方向 | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
语种 | 英语 |
WOS记录号 | WOS:000450038900012 |
内容类型 | 期刊论文 |
版本 | 出版稿 |
源URL | [http://202.127.25.143/handle/331003/3466] |
专题 | 生化所2018年发文 上海生化细胞研究所_上海生科院生化细胞研究所 |
通讯作者 | Huan, Haiyan; Chen, Luonan |
作者单位 | 1.Renmin Univ China, Sch Informat, Dept Math, Beijing 100872, Peoples R China; 2.Univ Calif Berkeley, Dept Mech Engn, Berkeley, CA 94720 USA; 3.Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA; 4.Chinese Acad Sci, CAS Ctr Excellence Mol Cell Sci, Inst Biochem & Cell Biol, Key Lab Syst Biol,Shanghai Inst Biol Sci, Shanghai 200031, Peoples R China; 5.Chinese Acad Sci, CAS Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China |
推荐引用方式 GB/T 7714 | Jiang, Hao,Sohn, Lydia L.,Huan, Haiyan,et al. Single cell clustering based on cell-pair differentiability correlation and variance analysis[J]. BIOINFORMATICS,2018,34(21):3684-3694. |
APA | Jiang, Hao,Sohn, Lydia L.,Huan, Haiyan,&Chen, Luonan.(2018).Single cell clustering based on cell-pair differentiability correlation and variance analysis.BIOINFORMATICS,34(21),3684-3694. |
MLA | Jiang, Hao,et al."Single cell clustering based on cell-pair differentiability correlation and variance analysis".BIOINFORMATICS 34.21(2018):3684-3694. |
个性服务 |
查看访问统计 |
相关权益政策 |
暂无数据 |
收藏/分享 |
除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。
修改评论