生物学家通常使用本体论系统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序。因此,与表型相关的重要分子功能类别可以在本体系统中方便地查看。自GO(GeneOntology)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。在这里,我们提供了由MATLAB开发的丰富计算应用程序oppOntology(OmicsPilotPlatformforOntology)。oppOntology支持同时计算具有歧管富集分数的多个样本(GeneCount,GeneRatio,EnrichFactor,HypergeometricTest,和FisherExactTest)。OppOntology不仅可以计算通用功能数据库的富集分数,比如GO,KEGG,HPO,和MsigDB,而且还用于自定义的功能类别数据库和定制的GOSlim。此外,oppOntology支持以批处理方式在线映射KEGG通路图。opOntology的GUI(图形用户界面)是在MATLAB中AppDesigner的架构上开发的,并且所有输入和输出文件都是MicrosoftExcel。OppOntology是一个独立的,易于使用的富集计算软件,可以在https://github.com/HangZhoep/oppOntology上获得。
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 .