Ge Sheng-Yang, Wang Ze-Ning, Sun Chuan-Yu, Tan Yi-Fan, Jin Hong, Zhang Yang
Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
Appl Biochem Biotechnol. 2023 Feb;195(2):832-843. doi: 10.1007/s12010-022-04170-6. Epub 2022 Oct 7.
Biologists often use systems of ontologies to classify gene lists obtained by high-throughput gene or protein-sequencing instruments, and then enrichment scores were used to rank the ontology system. Therefore, the important molecular functional categories related to the phenotype can be conveniently viewed in the ontology system. Since the birth of GO (Gene Ontology) organization, various types of ontology software have been developed to calculate enrichment scores for the target gene list in the GO system. Herein, we provide an enrichment calculation application oppOntology (Omics Pilot Platform for Ontology) developed by MATLAB. oppOntology supports simultaneous calculation of multiple samples with manifold enrichment scores (GeneCount, GeneRatio, EnrichFactor, HypergeometricTest, and FisherExactTest). oppOntology can not only calculate enrichment scores for generic functional databases, such as GO, KEGG, HPO, and MsigDB, but also for self-defined functional category databases and customized GO Slim. Moreover, oppOntology supports online mapping of KEGG pathway diagrams in a batch way. The GUI (Graphical User Interface) of oppOntology is developed on the architecture of AppDesigner in MATLAB, and all input and output files are Microsoft Excel. oppOntology is an independent, easy-to-use enrichment calculation software, that can be available at https://github.com/HangZhouSheep/oppOntology .
生物学家经常使用本体系统来对通过高通量基因或蛋白质测序仪器获得的基因列表进行分类，然后使用富集分数对本体系统进行排名。因此，可以在本体系统中方便地查看与表型相关的重要分子功能类别。自基因本体（Gene Ontology，GO）组织诞生以来，已经开发了各种类型的本体软件来计算GO系统中目标基因列表的富集分数。在此，我们提供了一个由MATLAB开发的富集计算应用程序oppOntology（本体组学实验平台）。oppOntology支持同时计算多个样本的多种富集分数（基因计数、基因比例、富集因子、超几何检验和Fisher精确检验）。oppOntology不仅可以为通用功能数据库（如GO、KEGG、HPO和MsigDB）计算富集分数，还可以为自定义功能类别数据库和定制的GO Slim计算富集分数。此外，oppOntology支持批量在线映射KEGG通路图。oppOntology的图形用户界面（GUI）是在MATLAB的AppDesigner架构上开发的，所有输入和输出文件均为Microsoft Excel格式。oppOntology是一款独立且易于使用的富集计算软件，可在https://github.com/HangZhouSheep/oppOntology获取。
