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Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile

文献类型：期刊论文

作者Guan, Yuanfang1; Li, Tingyang1; Zhang, Hongjiu1; Zhu, Fan2; Omenn, Gilbert S.1,3,4,5
刊名BIOINFORMATICS
出版日期2018-12-01
卷号34期号:23页码:3975-3982
ISSN号1367-4803
DOI10.1093/bioinformatics/bty467
通讯作者Guan, Yuanfang(gyuanfan@umich.edu) ; Omenn, Gilbert S.()
英文摘要Motivation: Finding driver genes that are responsible for the aberrant proliferation rate of cancer cells is informative for both cancer research and the development of targeted drugs. The established experimental and computational methods are labor-intensive. To make algorithms feasible in real clinical settings, methods that can predict driver genes using less experimental data are urgently needed. Results: We designed an effective feature selection method and used Support Vector Machines (SVM) to predict the essentiality of the potential driver genes in cancer cell lines with only 10 genes as features. The accuracy of our predictions was the highest in the Broad-DREAM Gene Essentiality Prediction Challenge. We also found a set of genes whose essentiality could be predicted much more accurately than others, which we called Accurately Predicted (AP) genes. Our method can serve as a new way of assessing the essentiality of genes in cancer cells.
资助项目National Science Foundation[1452656] ; Alzheimer's Association[BAND-15-367116] ; National Institutes of Health[P30ES17885] ; National Institutes of Health[U24CA210967]
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
语种英语
WOS记录号WOS:000453453300003
出版者OXFORD UNIV PRESS
源URL[http://119.78.100.138/handle/2HOD01W0/7185]  
专题中国科学院重庆绿色智能技术研究院
通讯作者Guan, Yuanfang; Omenn, Gilbert S.
作者单位1.Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA
2.Chinese Acad Sci, Chongqing Inst Green & Intelligent Technol, Key Lab Big Data & Intelligent Comp, Chongqing 400714, Peoples R China
3.Univ Michigan, Dept Internal Med, Ann Arbor, MI 48109 USA
4.Univ Michigan, Dept Human Genet, Ann Arbor, MI 48109 USA
5.Univ Michigan, Sch Publ Hlth, Ann Arbor, MI 48109 USA
推荐引用方式
GB/T 7714		 Guan, Yuanfang,Li, Tingyang,Zhang, Hongjiu,et al. Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile[J]. BIOINFORMATICS,2018,34(23):3975-3982.
APA Guan, Yuanfang,Li, Tingyang,Zhang, Hongjiu,Zhu, Fan,&Omenn, Gilbert S..(2018).Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile.BIOINFORMATICS,34(23),3975-3982.
MLA Guan, Yuanfang,et al."Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile".BIOINFORMATICS 34.23(2018):3975-3982.

入库方式： OAI收割

来源：重庆绿色智能技术研究院

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