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. 2024 May 7;227(1):iyad211.
doi: 10.1093/genetics/iyad211.

FlyBase: updates to the Drosophila genes and genomes database

Arzu Öztürk-Çolak  1 , Steven J Marygold  1 , Giulia Antonazzo  1 , Helen Attrill  1 , Damien Goutte-Gattat  1 , Victoria K Jenkins  2 , Beverley B Matthews  2 , Gillian Millburn  1 , Gilberto Dos Santos  2 , Christopher J Tabone  2 ; FlyBase Consortium
Collaborators, Affiliations

FlyBase: updates to the Drosophila genes and genomes database

Arzu Öztürk-Çolak et al. Genetics. .

Abstract

FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction of single-cell RNA sequencing data, improved content and display of functional information, updated orthology pipelines, new chemical reports, and enhancements to our outreach resources.

Keywords: Drosophila; FlyBase; model organism database.

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Conflict of interest statement

Conflicts of interest: The author(s) declare no conflicts of interest.

Figures

Fig. 1.
Fig. 1.
Fly Cell Atlas scRNA-seq data in FlyBase. a) Expression Summary Ribbons subsection of the srp Gene Report showing Fly Cell Atlas scRNA-seq cell type ribbon. Each tile is colored depending on the proportion of cells of the indicated cell type in which the current gene is expressed, according to the Fly Cell Atlas dataset. b) High-Throughput Expression Data subsection of the srp Gene Report showing Fly Cell Atlas bar chart. For each high-level cell type, this graph displays both the proportion of expressing cells and the average level of expression in all cells that do express the gene. c) The Term Report page for the “adult crystal cell” cell type. Clicking on the “Libraries/Collections” button brings up the list of all scRNA-seq clusters in which adult crystal cells have been identified.
Fig. 2.
Fig. 2.
New tools to explore genes from a HitList in FlyBase. a) QuickSearch query for alleles that have a phenotype manifesting in the Johnston organ, gives a HitList of alleles that can be converted into b) a list of genes and exported to c) the GO Ribbon Stack Viewer tool to compare the GO annotations. d) A list of genes exported to the PANGEA tool where e) enrichment over various classifications can be computed and visualized.
Fig. 3.
Fig. 3.
Newly added functional data in FlyBase. a) Catalytic Activity subsection of the Pfk Gene Report showing EC and Rhea information. b) Structure subsection of the 18w Gene Report showing protein structure predicted by AlphaFold. c) Structure subsection of the tRNA:Asn-GTT-1-9 Gene Report showing ncRNA structure predicted by R2DT.
Fig. 4.
Fig. 4.
Variant Molecular Consequences in FlyBase. Variant Molecular Consequences subsection of aurA Gene Report.
Fig. 5.
Fig. 5.
Chemical Reports in FlyBase. Bortezomib Chemical Report.
See this image and copyright information in PMC

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