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  2. 昆明动物研究所
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  4. 动物模型与人类重大疾病机理重点实验室
A Normalization-Free and Nonparametric Method Sharpens Large-Scale Transcriptome Analysis and Reveals Common Gene Alteration Patterns in Cancers

文献类型：期刊论文

作者Li QG3,8; ybchen@mail.kiz.ac.cn; kongqp@mail.kiz.ac.cn; Pu SY3,8; Yang CP2; Kong QP*3,8; Wu H3,7,8; Chen YB*2; Zhou JM2; Li HP9
刊名Theranostics
出版日期2017
卷号7期号:11页码:2888-2899
关键词Cross-value Association Analysis Normalization-free Pan-cancer Transcriptome Heterogeneity
英文摘要Heterogeneity in transcriptional data hampers the identification of differentially expressed genes (DEGs) and understanding of cancer, essentially because current methods rely on cross-sample normalization and/or distribution assumption—both sensitive to heterogeneous values. Here, we developed a new method, Cross-Value Association Analysis (CVAA), which overcomes the limitation and is more robust to heterogeneous data than the other methods. Applying CVAA to a more complex pan-cancer dataset containing 5,540 transcriptomes discovered numerous new DEGs and many previously rarely explored pathways/processes; some of them were validated, both in vitro and in vivo, to be crucial in tumorigenesis, e.g., alcohol metabolism (ADH1B), chromosome remodeling (NCAPH) and complement system (Adipsin). Together, we present a sharper tool to navigate large-scale expression data and gain new mechanistic insights into tumorigenesis.
语种英语
资助机构This work was supported by the Key Research Program of the Chinese Academy of Sciences (Grant NO. KJZD-EW-L14), grants from the Chinese Academy of Sciences (QYZDB-SSW-SMC020), the National Natural Science Foundation of China (81272309, 81322030, U1502224, 81672764, 31271579, 81602346, 81671404, 81500670), Yunnan Applied Basic Research Projects (2014FA038), and grant from the Youth Innovation Promotion Association of Chinese Academy of Sciences (to Y.H. He). ; This work was supported by the Key Research Program of the Chinese Academy of Sciences (Grant NO. KJZD-EW-L14), grants from the Chinese Academy of Sciences (QYZDB-SSW-SMC020), the National Natural Science Foundation of China (81272309, 81322030, U1502224, 81672764, 31271579, 81602346, 81671404, 81500670), Yunnan Applied Basic Research Projects (2014FA038), and grant from the Youth Innovation Promotion Association of Chinese Academy of Sciences (to Y.H. He). ; This work was supported by the Key Research Program of the Chinese Academy of Sciences (Grant NO. KJZD-EW-L14), grants from the Chinese Academy of Sciences (QYZDB-SSW-SMC020), the National Natural Science Foundation of China (81272309, 81322030, U1502224, 81672764, 31271579, 81602346, 81671404, 81500670), Yunnan Applied Basic Research Projects (2014FA038), and grant from the Youth Innovation Promotion Association of Chinese Academy of Sciences (to Y.H. He). ; This work was supported by the Key Research Program of the Chinese Academy of Sciences (Grant NO. KJZD-EW-L14), grants from the Chinese Academy of Sciences (QYZDB-SSW-SMC020), the National Natural Science Foundation of China (81272309, 81322030, U1502224, 81672764, 31271579, 81602346, 81671404, 81500670), Yunnan Applied Basic Research Projects (2014FA038), and grant from the Youth Innovation Promotion Association of Chinese Academy of Sciences (to Y.H. He).
源URL[http://159.226.149.26:8080/handle/152453/11821]  
专题昆明动物研究所_动物模型与人类重大疾病机理重点实验室
昆明动物研究所_遗传资源与进化国家重点实验室
昆明动物研究所_分子人类学
昆明动物研究所_肿瘤信号转导
昆明动物研究所_基因调控与表达遗传
通讯作者ybchen@mail.kiz.ac.cn; kongqp@mail.kiz.ac.cn
作者单位1.School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
2.Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
3.KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
4.Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha 410013, China
5.Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
6.Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
7.Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.
8.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
9.Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
推荐引用方式
GB/T 7714		 Li QG,ybchen@mail.kiz.ac.cn,kongqp@mail.kiz.ac.cn,et al. A Normalization-Free and Nonparametric Method Sharpens Large-Scale Transcriptome Analysis and Reveals Common Gene Alteration Patterns in Cancers[J]. Theranostics,2017,7(11):2888-2899.
APA Li QG.,ybchen@mail.kiz.ac.cn.,kongqp@mail.kiz.ac.cn.,Pu SY.,Yang CP.,...&He YH.(2017).A Normalization-Free and Nonparametric Method Sharpens Large-Scale Transcriptome Analysis and Reveals Common Gene Alteration Patterns in Cancers.Theranostics,7(11),2888-2899.
MLA Li QG,et al."A Normalization-Free and Nonparametric Method Sharpens Large-Scale Transcriptome Analysis and Reveals Common Gene Alteration Patterns in Cancers".Theranostics 7.11(2017):2888-2899.

入库方式： OAI收割

来源：昆明动物研究所

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