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Using FlyBase to Find Functionally Related Drosophila Genes.

Alix J Rey1, Helen Attrill2, Steven J Marygold2

  • 1Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK. alix.j.rey@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|May 16, 2018
PubMed
Summary
This summary is machine-generated.

FlyBase provides tools to find functionally related genes in Drosophila melanogaster using Gene Ontology annotations and protein domain data. This facilitates the analysis of gene sets for biological research.

Keywords:
D. melanogasterDatabaseDrosophilaFlyBaseFunctionally related genesGene OntologyGene groupProtein domain

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Area of Science:

  • Genomics
  • Bioinformatics
  • Model Organisms

Background:

  • FlyBase has been a primary resource for Drosophila melanogaster genetic information for over 25 years.
  • Traditional gene-by-gene data presentation is limiting for analyzing functionally related gene sets in the genomic era.

Purpose of the Study:

  • To describe methods for generating lists of functionally related genes in FlyBase.
  • To guide users in analyzing these gene sets.

Main Methods:

  • Utilizing Gene Ontology (GO) annotations within FlyBase.
  • Leveraging protein domain data for gene set compilation.
  • Employing preassembled "Gene Group" reports curated from literature and expert databases.

Main Results:

  • Protocols are detailed for extracting gene lists based on GO terms and protein domains.
  • FlyBase "Gene Groups" offer manually curated, functionally related gene sets.
  • Guidance is provided for subsequent analysis and processing of these gene lists.

Conclusions:

  • FlyBase offers multiple strategies for identifying and analyzing functionally related gene sets.
  • These resources enhance the study of gene function and biological pathways in Drosophila.
  • The described protocols empower researchers to leverage FlyBase for complex genomic analyses.