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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. KOBAS can be freely accessed at http:\/\/kobas.cbi.pku.edu.cn, and a mirror site is available at http:\/\/bioinfo.org\/kobas.<\/jats:p>","DOI":"10.1093\/nar\/gkab447","type":"journal-article","created":{"date-parts":[[2021,5,9]],"date-time":"2021-05-09T11:07:34Z","timestamp":1620558454000},"page":"W317-W325","source":"Crossref","is-referenced-by-count":1628,"title":["KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis"],"prefix":"10.1093","volume":"49","author":[{"given":"Dechao","family":"Bu","sequence":"first","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy ofSciences, Beijing, 100190, China"}]},{"given":"Haitao","family":"Luo","sequence":"additional","affiliation":[{"name":"Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China"}]},{"given":"Peipei","family":"Huo","sequence":"additional","affiliation":[{"name":"Chinese Academy of Sciences, LuoYang Branch of Institute of Computing Technology, Luoyang, 471000,\u00a0China"}]},{"given":"Zhihao","family":"Wang","sequence":"additional","affiliation":[{"name":"Chinese Academy of Sciences, LuoYang Branch of Institute of Computing Technology, Luoyang, 471000,\u00a0China"}]},{"given":"Shan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Chinese Academy of Sciences, LuoYang Branch of Institute of Computing Technology, Luoyang, 471000,\u00a0China"}]},{"given":"Zihao","family":"He","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, ChaoYang District, Beijing 100029, China"}]},{"given":"Yang","family":"Wu","sequence":"additional","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy ofSciences, Beijing, 100190, China"}]},{"given":"Lianhe","family":"Zhao","sequence":"additional","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy ofSciences, Beijing, 100190, China"}]},{"given":"Jingjia","family":"Liu","sequence":"additional","affiliation":[{"name":"Cancer Center, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Zhejiang 315000, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5616-6910","authenticated-orcid":false,"given":"Jincheng","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, ChaoYang District, Beijing 100029, China"}]},{"given":"Shuangsang","family":"Fang","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, ChaoYang District, Beijing 100029, China"}]},{"given":"Wanchen","family":"Cao","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, ChaoYang District, Beijing 100029, China"}]},{"given":"Lan","family":"Yi","sequence":"additional","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy ofSciences, Beijing, 100190, China"}]},{"given":"Yi","family":"Zhao","sequence":"additional","affiliation":[{"name":"Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy ofSciences, Beijing, 100190, China"}]},{"given":"Lei","family":"Kong","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China"}]}],"member":"286","published-online":{"date-parts":[[2021,6,4]]},"reference":[{"key":"2021070812152412200_B1","doi-asserted-by":"crossref","first-page":"e1002375","DOI":"10.1371\/journal.pcbi.1002375","article-title":"Ten years of pathway analysis: current approaches and outstanding challenges","volume":"8","author":"Khatri","year":"2012","journal-title":"PLoS Comput. 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