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oppOntology: a MATLAB Toolbox for Enrichment Analysis.

Sheng-Yang Ge1, Ze-Ning Wang2, Chuan-Yu Sun1

  • 1Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, China.

Applied Biochemistry and Biotechnology
|October 7, 2022
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Summary
This summary is machine-generated.

oppOntology is a new MATLAB tool for calculating gene list enrichment scores using various ontologies. This omics software aids biologists in identifying key molecular functions related to phenotypes from high-throughput sequencing data.

Keywords:
EnrichmentGraphical User InterfaceMATLAB AppDesignerOmics Pilot Platform of OntologyVisualizationoppOntology

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biologists utilize ontology systems to classify gene lists from high-throughput sequencing.
  • Enrichment scores are crucial for ranking these ontologies and identifying phenotype-related molecular functions.
  • Existing software for calculating Gene Ontology (GO) enrichment scores has limitations.

Purpose of the Study:

  • To introduce oppOntology (Omics Pilot Platform for Ontology), a novel MATLAB-based application for enrichment score calculation.
  • To provide a user-friendly tool that supports multiple samples and various enrichment metrics.
  • To enable analysis across diverse functional databases and custom ontologies.

Main Methods:

  • Developed oppOntology using MATLAB's AppDesigner for a graphical user interface (GUI).
  • Implemented simultaneous calculation for multiple samples with multiple enrichment scores (GeneCount, GeneRatio, EnrichFactor, HypergeometricTest, FisherExactTest).
  • Integrated support for standard databases (GO, KEGG, HPO, MsigDB) and custom databases/GO Slim, with batch KEGG pathway mapping.

Main Results:

  • oppOntology offers simultaneous enrichment calculations for multiple samples and scores.
  • The software supports a wide range of generic and custom functional databases.
  • It provides batch online mapping of KEGG pathway diagrams and uses Excel for input/output.

Conclusions:

  • oppOntology is a versatile, independent, and user-friendly enrichment calculation software.
  • It simplifies the identification of significant molecular functional categories from omics data.
  • The tool is readily available for the research community.