• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

KOBAS-i：用于基因富集分析的生物学功能智能优先级排序和探索性可视化。

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

机构信息

Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy ofSciences, Beijing, 100190, China.

Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China.

出版信息

Nucleic Acids Res. 2021 Jul 2;49(W1):W317-W325. doi: 10.1093/nar/gkab447.

DOI:10.1093/nar/gkab447
PMID:34086934
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8265193/
Abstract

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. KOBAS can be freely accessed at http://kobas.cbi.pku.edu.cn, and a mirror site is available at http://bioinfo.org/kobas.

摘要

基因集富集（GSE）分析在从全基因组实验中提取生物学见解方面起着至关重要的作用。ORA（过表达分析）、FCS（功能类别评分）和 PT（途径拓扑）方法是沿着发展时间线的三代 GSE 方法。以前版本的 KOBAS 仅基于 ORA 方法提供服务。在这里，我们展示了 KOBAS 的 3.0 版本，称为 KOBAS-i（KOBAS 智能版的缩写）。它引入了我们之前发布的一种基于机器学习的新方法 CGPS，它将七种 FCS 工具和两种 PT 工具整合到一个单一的集成评分中，并智能地优先考虑相关的生物途径。此外，KOBAS 还扩展了下游探索性可视化功能，用于选择和理解丰富的结果。该工具构建了 cirFunMap 的新视图，以景观的形式呈现不同的丰富术语及其相关性。最后，基于前一版本的框架，KOBAS 将支持的物种数量从 1327 种增加到 5944 种。为了更方便地在本地运行，它还提供了一个预先构建的 Docker 镜像，无需安装，作为源代码版本的补充。KOBAS 可在 http://kobas.cbi.pku.edu.cn 上免费访问，镜像站点可在 http://bioinfo.org/kobas 上访问。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/2330f4eb93ae/gkab447fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/a498f78fe97d/gkab447gra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/7ea53c355c17/gkab447fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/82bc03d13a38/gkab447fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/9f0386a9cd0c/gkab447fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/2330f4eb93ae/gkab447fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/a498f78fe97d/gkab447gra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/7ea53c355c17/gkab447fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/82bc03d13a38/gkab447fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/9f0386a9cd0c/gkab447fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a50e/8265193/2330f4eb93ae/gkab447fig4.jpg

相似文献

1
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis.KOBAS-i：用于基因富集分析的生物学功能智能优先级排序和探索性可视化。
Nucleic Acids Res. 2021 Jul 2;49(W1):W317-W325. doi: 10.1093/nar/gkab447.
2
CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways.CGPS：一种基于机器学习的方法，整合了多种基因集分析工具，以便更好地对生物学相关途径进行优先级排序。
J Genet Genomics. 2018 Sep 20;45(9):489-504. doi: 10.1016/j.jgg.2018.08.002. Epub 2018 Sep 13.
3
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.KOBAS 2.0：一个用于注释和识别富集通路和疾病的网络服务器。
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W316-22. doi: 10.1093/nar/gkr483.
4
KOBAS server: a web-based platform for automated annotation and pathway identification.KOBAS服务器：一个基于网络的自动注释和通路识别平台。
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W720-4. doi: 10.1093/nar/gkl167.
5
Computing and Visualizing Gene Function Similarity and Coherence with NaviGO.使用NaviGO计算和可视化基因功能的相似性与连贯性。
Methods Mol Biol. 2018;1807:113-130. doi: 10.1007/978-1-4939-8561-6_9.
6
DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.DOSE：一个用于疾病本体语义和富集分析的R/Bioconductor软件包。
Bioinformatics. 2015 Feb 15;31(4):608-9. doi: 10.1093/bioinformatics/btu684. Epub 2014 Oct 17.
7
GSDS 2.0: an upgraded gene feature visualization server.基因结构显示服务器2.0：一个升级的基因特征可视化服务器。
Bioinformatics. 2015 Apr 15;31(8):1296-7. doi: 10.1093/bioinformatics/btu817. Epub 2014 Dec 10.
8
FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis.FunSet：一个用于执行和展示基因本体论富集分析的开源软件和网络服务器。
BMC Bioinformatics. 2019 Jun 27;20(1):359. doi: 10.1186/s12859-019-2960-9.
9
An improved catalogue of putative synaptic genes defined exclusively by temporal transcription profiles through an ensemble machine learning approach.通过集成机器学习方法，根据时间转录谱专门定义的假定突触基因的改良目录。
BMC Genomics. 2019 Dec 23;20(1):1011. doi: 10.1186/s12864-019-6380-z.
10
NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies.NeVOmics：一种用于基因本体论和功能网络分析以及对来自组学技术的数据进行可视化的富集工具。
Genes (Basel). 2018 Nov 23;9(12):569. doi: 10.3390/genes9120569.

引用本文的文献

1
Whole genome duplication drives transcriptome reprogramming in response to drought in alfalfa.全基因组复制驱动紫花苜蓿响应干旱时的转录组重编程。
Plant Cell Rep. 2025 Sep 9;44(10):209. doi: 10.1007/s00299-025-03593-9.
2
Transcriptomic Analysis Reveals Key Regulatory Genes and Pathways Involved in Macrophage Inflammation Induced by Hypervirulent Klebsiella pneumoniae Infection.转录组分析揭示了高毒力肺炎克雷伯菌感染诱导巨噬细胞炎症反应中涉及的关键调控基因和信号通路。
Curr Microbiol. 2025 Sep 5;82(10):492. doi: 10.1007/s00284-025-04481-x.
3
Deciphering the Gene Expression and Alternative Splicing Basis of Muscle Development Through Interpretable Machine Learning Models.

本文引用的文献

1
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.PANTHER 版本 16：修订后的家族分类、基于树的分类工具、增强子区域和广泛的 API。
Nucleic Acids Res. 2021 Jan 8;49(D1):D394-D403. doi: 10.1093/nar/gkaa1106.
2
The Gene Ontology resource: enriching a GOld mine.基因本体论资源：丰富一个 GOld 矿。
Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334. doi: 10.1093/nar/gkaa1113.
3
GeneTrail 3: advanced high-throughput enrichment analysis.Genetrail 3：高级高通量富集分析。
通过可解释的机器学习模型解析肌肉发育的基因表达和可变剪接基础
Biology (Basel). 2025 Aug 15;14(8):1059. doi: 10.3390/biology14081059.
4
Squama Manitis Extract Exhibits Broad-Spectrum Antibacterial Activity Through Energy and DNA Disruption Mechanisms.穿山甲鳞片提取物通过能量和DNA破坏机制展现出广谱抗菌活性。
Biology (Basel). 2025 Jul 28;14(8):949. doi: 10.3390/biology14080949.
5
Identification of progression-related genes and construction of prognostic model for chronic kidney disease by machine learning.通过机器学习识别慢性肾脏病进展相关基因并构建预后模型
Front Cell Dev Biol. 2025 Aug 15;13:1627355. doi: 10.3389/fcell.2025.1627355. eCollection 2025.
6
1-Aminocyclopropane-1-carboxylic acid induces resource reallocation in sporophytes.1-氨基环丙烷-1-羧酸诱导孢子体中的资源重新分配。
Front Plant Sci. 2025 Aug 15;16:1632530. doi: 10.3389/fpls.2025.1632530. eCollection 2025.
7
Genomic and transcriptomic data reveal molecular differences between homologous recombination deficiency subgroups in Chinese ovarian cancer patients.基因组和转录组数据揭示了中国卵巢癌患者同源重组缺陷亚组之间的分子差异。
Hum Genomics. 2025 Aug 31;19(1):104. doi: 10.1186/s40246-025-00806-w.
8
Identification of a dominant stripe rust resistance gene YrXY on chromosome 6R in hexaploid triticale.六倍体小黑麦6R染色体上一个显性抗条锈病基因YrXY的鉴定
Theor Appl Genet. 2025 Aug 30;138(9):234. doi: 10.1007/s00122-025-05025-4.
9
Transcriptome Analysis of Developmental Gene Expression in Turcz.地锦发育基因表达的转录组分析
Plants (Basel). 2025 Aug 16;14(16):2549. doi: 10.3390/plants14162549.
10
Integrating Full-Length and Second-Generation Transcriptomes to Elucidate the ApNPV-Induced Transcriptional Reprogramming in Midgut.整合全长转录组和第二代转录组以阐明苜蓿银纹夜蛾核多角体病毒诱导的中肠转录重编程
Insects. 2025 Jul 31;16(8):792. doi: 10.3390/insects16080792.
Nucleic Acids Res. 2020 Jul 2;48(W1):W515-W520. doi: 10.1093/nar/gkaa306.
4
The clinical promise of biomarkers of synapse damage or loss in Alzheimer's disease.阿尔茨海默病中突触损伤或丢失的生物标志物的临床前景。
Alzheimers Res Ther. 2020 Mar 2;12(1):21. doi: 10.1186/s13195-020-00588-4.
5
Toward a gold standard for benchmarking gene set enrichment analysis.迈向基因集富集分析基准测试的金标准。
Brief Bioinform. 2021 Jan 18;22(1):545-556. doi: 10.1093/bib/bbz158.
6
The reactome pathway knowledgebase.Reactome 通路知识库。
Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031.
7
WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs.WebGestalt 2019：基因集分析工具包，具有全新的用户界面和 API。
Nucleic Acids Res. 2019 Jul 2;47(W1):W199-W205. doi: 10.1093/nar/gkz401.
8
modEnrichr: a suite of gene set enrichment analysis tools for model organisms.modEnrichr：一套适用于模式生物的基因集富集分析工具。
Nucleic Acids Res. 2019 Jul 2;47(W1):W183-W190. doi: 10.1093/nar/gkz347.
9
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).g:Profiler：一个用于功能富集分析和基因列表转换的网络服务器（2019 更新）。
Nucleic Acids Res. 2019 Jul 2;47(W1):W191-W198. doi: 10.1093/nar/gkz369.
10
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.Metascape 为系统水平数据集的分析提供了面向生物学家的资源。
Nat Commun. 2019 Apr 3;10(1):1523. doi: 10.1038/s41467-019-09234-6.