KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

doi:10.1093/nar/gkab447

	KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis
	Bu, Dechao 1; Luo, Haitao 3; Huo, Peipei 4; Wang, Zhihao 4; Zhang, Shan 4; He, Zihao 5; Wu, Yang 1; Zhao, Lianhe 1; Liu, Jingjia 6; Guo, Jincheng 5; Fang, Shuangsang 5; Cao, Wanchen 5; Yi, Lan 1; Zhao, Yi 1; Kong, Lei 2
	2021-07-02
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	49 期号:W1 页码:W317-W325
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.
DOI	10.1093/nar/gkab447
收录类别	SCI
语种	英语
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
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000672775800042
出版者	OXFORD UNIV PRESS
引用统计	被引频次：633[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/17474
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.