GOReverseLookup: A gene ontology reverse lookup tool.

Journal: Computers in biology and medicine
PMID: 40239235

Abstract

BACKGROUND AND OBJECTIVE: The Gene Ontology (GO) project has been pivotal in providing a structured framework for characterizing genes and annotating them to specific biological concepts. While traditional gene annotation primarily focuses on mapping genes to GO terms, descriptors of biological concepts, there is a growing need for tools facilitating reverse querying. This paper introduces GOReverseLookup, a novel tool designed to identify over- or underrepresented genes in researcher-defined states of interest (phenotypes), described by sets of GO terms. GOReverseLookup supplements the existing power of Gene Ontology by the possibility of orthologous gene querying across several databases, such as Ensembl and UniProtKB. This combination allows for a more nuanced identification of significant genes across a range of cross-species research contexts.

Authors

  • Aljoša Škorjanc
    Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana, Slovenia.
  • Vladimir Smrkolj
    Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana, Slovenia; National Institute of Chemistry, Hajdrihova ulica 19, Ljubljana, Slovenia.
  • Nejc Umek
    Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana, Slovenia. Electronic address: nejc.umek@mf.uni-lj.si.

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