中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
首页 机构 成果 学者
  
  1. CAS IR Grid
  2. 计算技术研究所
  3. 中国科学院计算技术研究所
  4. 中国科学院计算技术研究所期刊论文
  5. 英文
热门
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

文献类型：期刊论文

作者Bu, Dechao1; Luo, Haitao3; Huo, Peipei4; Wang, Zhihao4; Zhang, Shan4; He, Zihao5; Wu, Yang1; Zhao, Lianhe1; Liu, Jingjia6; Guo, Jincheng5
刊名NUCLEIC ACIDS RESEARCH
出版日期2021-07-02
卷号49期号:W1页码:W317-W325
ISSN号0305-1048
DOI10.1093/nar/gkab447
英文摘要Gene set enrichment (GSE) analysis plays an essential role in extracting biological insight from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class scoring), and PT (pathway topology) approaches are three generations of GSE methods along the timeline of development. Previous versions of KOBAS provided services based on just the ORA method. Here we presented version 3.0 of KOBAS, which is named KOBAS-i (short for KOBAS intelligent version). It introduced a novel machine learning-based method we published earlier, CGPS, which incorporates seven FCS tools and two PT tools into a single ensemble score and intelligently prioritizes the relevant biological pathways. In addition, KOBAS has expanded the downstream exploratory visualization for selecting and understanding the enriched results. The tool constructs a novel view of cirFunMap, which presents different enriched terms and their correlations in a landscape. Finally, based on the previous version's framework, KOBAS increased the number of supported species from 1327 to 5944. For an easier local run, it also provides a prebuilt Docker image that requires no installation, as a supplementary to the source code version.
资助项目National Key R&D Program of China[2016YFB0201700] ; National Key R&D Program of China[2017YFC0908404] ; National Natural Science Foundation of Zhejiang Province[LY20C060001] ; National Natural Science Foundation of Zhejiang Province[LY21C060003] ; The National Natural Science Foundation of China[32070670] ; Zhejiang Provincial Research Center for Cancer Intelligent Diagnosis and Molecular Technology[JBZX-20200] ; National Natural Science Foundation for Young Scholars of China[31701149] ; National Natural Science Foundation for Young Scholars of China[31701141]
WOS研究方向Biochemistry & Molecular Biology
语种英语
出版者OXFORD UNIV PRESS
WOS记录号WOS:000672775800042
源URL[http://119.78.100.204/handle/2XEOYT63/17473]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Zhao, Yi; Kong, Lei
作者单位1.Chinese Acad Sci, Pervas Comp Res Ctr, Inst Comp Technol, China 100190, Peoples R China
2.Peking Univ, Sch Life Sci, Ctr Bioinformat, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China
3.Jinan Univ, Shenzhen Peoples Hosp, Clin Med Coll 2, Translat Med Collaborat Innovat Ctr, Shenzhen 518020, Peoples R China
4.Chinese Acad Sci, Inst Comp Technol, LuoYang Branch, Luoyang 471000, Peoples R China
5.Beijing Univ Chinese Med, Sch Tradit Chinese Med, Beijing 100029, Peoples R China
6.Univ Chinese Acad Sci, Ningbo Inst Life & Hlth Ind, Canc Ctr, Ningbo 315000, Zhejiang, Peoples R China
推荐引用方式
GB/T 7714		 Bu, Dechao,Luo, Haitao,Huo, Peipei,et al. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis[J]. NUCLEIC ACIDS RESEARCH,2021,49(W1):W317-W325.
APA Bu, Dechao.,Luo, Haitao.,Huo, Peipei.,Wang, Zhihao.,Zhang, Shan.,...&Kong, Lei.(2021).KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis.NUCLEIC ACIDS RESEARCH,49(W1),W317-W325.
MLA Bu, Dechao,et al."KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis".NUCLEIC ACIDS RESEARCH 49.W1(2021):W317-W325.

入库方式： OAI收割

来源：计算技术研究所

浏览0
下载0
收藏0
其他版本

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。