Abstract
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.
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Data Availability
The program and full instruction of oppOntology was available at https://github.com/HangZhouSheep/oppOntology.
Abbreviations
- GO:
-
Gene Ontology
- DAVID:
-
Database for Annotation, Visualization and Integrated Discovery
- DEGs:
-
Differential Expressed Genes
- GSEA:
-
Gene Set Enrichment Analysis
- GUI:
-
Graphical User Interface
- HPO:
-
Human Phenotype Ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- MsigDB:
-
Molecular Signatures Database
- OPP:
-
Omics Pilot Platform
- oppOntology:
-
Omics Pilot Platform for Ontology
- REST:
-
Representational State Transfer
- URL:
-
Uniform Resource Locator
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Acknowledgements
We thank Dr. Yang Zhang for writing oppOntology independently. We are so grateful to the selfless help from the Shanghai Huisen Science & Technology Company for oppOntology maintenance.
Funding
This research was supported by the National Key R&D Program of China (2021YFF0703702) and the National Nature Science Foundation of China (32070605).
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Conception and design: Shengyang Ge and Yang Zhang.
Administrative support: Chuanyu Sun and Yang Zhang
Collection and assembly of data: Yang Zhang and Yi-fan Tan
Data analysis and interpretation: Yang Zhang and Zening Wang
Program writing: Yang Zhang
Manuscript writing: all authors
Final approval of manuscript: all authors
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Ge, Sy., Wang, Zn., Sun, Cy. et al. oppOntology: a MATLAB Toolbox for Enrichment Analysis. Appl Biochem Biotechnol 195, 832–843 (2023). https://doi.org/10.1007/s12010-022-04170-6
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DOI: https://doi.org/10.1007/s12010-022-04170-6