Gene Groups
There has been significant reorganisation of gene groups to untangle discrete macromolecular complexes from other gene groups in the hierarchy.
New groups added this release include THIOESTER-CONTAINING PROTEINS, PRELI-DOMAIN PROTEINS and SMALL TIMS.

New Metabolic Pathway Reports
New metabolic reports in this release cover AMINO ACID DERIVATIVE METABOLISM (7 reports), NEUROTRANSMITTER METABOLISM (8 reports), PIGMENT BIOSYNTHESIS (4 reports), KETOGENESIS and KETOLYSIS.

Updates to Gene Groups
New gene groups in this release include HOST DEFENSE PEPTIDES, NUCLEAR EXOSOME TARGETING COMPLEX and MITOCHONDRIAL INTERMEMBRANE SPACE TIM CHAPERONE COMPLEXES.

New Metabolic Pathway Reports
New metabolic reports include
L-VALINE CATABOLISM, L-ISOLEUCINE CATABOLISM, L-LEUCINE CATABOLISM, L-LYSINE CATABOLISM,
L-METHIONINE CYCLE, L-METHIONINE SALVAGE PATHWAY,
L-CYSTEINE BIOSYNTHESIS, L-PROLINE BIOSYNTHESIS, L-SERINE BIOSYNTHESIS, GLYCINE BIOSYNTHESIS,
GLYCINE CLEAVAGE SYSTEM,
L-PHENYLALANINE AND L-TYROSINE METABOLISM, L-ASPARTATE AND L-ASPARAGINE METABOLISM, L-GLUTAMATE AND L-GLUTAMINE METABOLISM,
L-GLUTAMATE BIOSYNTHESIS (FROM L-PROLINE),
L-ALANINE METABOLISM, L-ARGININE METABOLISM,
L-TRYPTOPHAN CATABOLISM and
AMINO ACID METABOLISM pathways.

Updates to FlyCyc
We have recently updated FlyCyc, the pathway-genome database representing Drosophila metabolism, to include enzymatic complexes as well as further improvements to enzyme annotations. FlyCyc is now classed as a ‘Tier 1 Highly Curated Organism Database’. Links from FlyBase gene reports to FlyCyc pathway pages have been updated to reflect the latest associations.

• European labs: Please consider contributing to the Cambridge, U.K. FlyBase group

• U.S. and other non-European labs: Please consider contributing to the U.S. FlyBase groups

• Both U.K. and U.S. FlyBase are working diligently to establish an invoicing system. We appreciate your continued patience.

For more information on how to support us, please visit: https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase

• Aberrations - gene deletion/duplication data

• Split system combinations

• Human disease model reports

• Single Cell RNA-Seq Metadata

• Gene model status and annotation comments

• Antibody information

• Disease-implicated variants

• Gene relationship comments

• InterPro signatures

• Representative publications

• Chemical Synonyms

• Curated Expression

A description of the contents and format of each file is found here.

New Metabolic Pathway Reports
New metabolic reports include the GLUCOSYLCERAMIDE BIOSYNTHESIS, the GPI-ANCHOR PROTEIN BIOSYNTHESIS and the DOLICHYL PHOSPHATE BIOSYNTHESIS pathways.

New Gene Group Reports
This release includes the mitochondrial complexes: MITOCHONDRIAL INNER MEMBRANE PEPTIDASE COMPLEX, MITOCHONDRIAL DEGRADOSOME and MITOCHONDRIAL PROCESSING PEPTIDASE. New family gene groups include, SPECTRINS and SINGLE VON WILLEBRAND FACTOR TYPE C DOMAIN PROTEINS.

Fly BLAST at the Alliance of Genome Resources
The Alliance of Genome Resources website has ‘beta’ released their new BLAST service, with Fly and Worm database sets. The fly database set comes from FlyBase, and will be updated with each FlyBase release. You can find a link to this BLAST service at FlyBase under Tools → Genomics Tools (see below), or you can go to the Alliance website and find a link under Data and Tools:

On the Alliance BLAST Service page, select the Fly BLAST link to go to the service page.

In May 2025, the NIH terminated all grant funding to Harvard University, including the NHGRI grant that supported FlyBase. This grant also funded FlyBase teams at Indiana University (IU) and the University of Cambridge (UK), and as a result, their subawards were also canceled.

The Cambridge team has secured support for one to two years through generous donations from the European fly community, emergency funding from the Wellcome Trust, and support from the University of Cambridge. At IU, funding has been secured for one year thanks to reserve funds from Thom Kaufman and a supplement from ORIP/NIH to the Bloomington Drosophila Stock Center (BDSC).

Unfortunately, the situation at Harvard is far more critical. Harvard University had supported FlyBase staff since May but recently denied a request for extended bridge funding. As a result, all eight employees (four full-time and four part-time) were abruptly laid off, with termination dates ranging from August to mid-October depending on their positions. In addition, our curator at the University of New Mexico will leave her position at the end of August. This decision came as a shock, and we are urgently pursuing all possible funding options.

To put the need into perspective: although FlyBase is free to use, it is not free to make. It takes large teams of people and millions of dollars a year to create FlyBase to support fly research (the last NHGRI grant supported us with more than 2 million USD per annum).

To help sustain FlyBase operations, we have been reaching out to you to ask for your support. We have set up a donation site in Cambridge, UK, to which European labs have and can continue to contribute, and a new donation site at IU to which labs in the US and the rest of the world can contribute. We urge researchers to work with their grant administrators to contribute to FlyBase via these sites if at all possible, as more of the money will go to FlyBase. However, we appreciate that some funding sources do not allow "donation" of research funds to FlyBase via these sites. We are therefore working to establish new "user access fee" systems at Cambridge UK and Indiana that will allow invoicing and the use of research funds, but several administrative issues must be resolved before they become active. While we previously collected user fees from Harvard, this was also stopped by the grant termination. For more information on how to donate, please see this Wiki page:

https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase

Our immediate goals are:

1. To maintain core curation activities and keep the FlyBase website online

2. To complete integration with the Alliance of Genome Resources (The Alliance).

Integration with the Alliance is essential for FlyBase’s long-term sustainability. For nearly a decade, NHGRI/NIH has supported the unification of Model Organism Databases (MODs) into the Alliance, which we aim to achieve by 2028. Therefore, securing bridge funding to sustain FlyBase over the next three years is crucial for successful integration and the long-term access to FlyBase data.

At present, our remaining funds will allow us to keep the FlyBase website online for approximately one more year. Beyond that, its future is uncertain unless new funding is secured. We will, of course, continue pursuing additional grant opportunities as they arise.

Given the uncertainty of future NIH or alternative funding sources, we are relying on the Fly community for support. Your contributions will directly help us retain the staff needed to complete this transition and to secure ongoing fly data curation into the Alliance beyond 2028.

We at FlyBase are incredibly grateful for the outpouring of support from the community during this challenging time. Your encouragement has strengthened our resolve and underscores how vital this resource remains to Drosophila research worldwide.

Sincerely,
The FlyBase Team

New metabolic reports include the ATR-ATRIP DNA DAMAGE-SENSING KINASE COMPLEX, the CHECKPOINT CLAMP COMPLEX, and the CYCLIN K-CDK12 COMPLEX.

New Metabolic Pathway reports

New metabolic reports include NUCLEOTIDE-SUGAR BIOSYNTHESIS, HEME BIOSYNTHESIS, IRON-SULFUR CLUSTER ASSEMBLY, Mo-MOLYBDOPTERIN COFACTOR BIOSYNTHESIS, UBIQUINONE BIOSYNTHESIS, PYRUVATE DECARBOXYLATION TO ACETYL-COA, TRICARBOXYLIC ACID (TCA) CYCLE, PROTEIN N-GLYCOSYLATION, DOLICHOL-LINKED OLIGOSACCHARIDE BIOSYNTHESIS, ENDOPLASMIC RETICULUM N-GLYCAN TRIMMING, GOLGI N-GLYCAN DIVERSIFICATION, and GOLGI N-GLYCAN TRIMMING.

We are pleased to announce that interactive tables are now available across all Gene Group class pages: Signaling Pathway, Metabolic Pathway, Macromolecular Complex and Gene Group reports. These interactive tables enable the customization of the ‘Members’ table, allowing column list sorting, filtering and column ordering. A menu of gene-associated data and reagents including Disease Models, Alleles, Transgenic construsts, GO Molecular Function, EC Enzyme Name and Cytogenetic map location, allows users to choose the display and downloading of information most suited to their requirements.

New precomputed files

Three new files have been added to our Bulk Downloads page.
Two of the files (Classical and insertion allele descriptions and Transgenic construct descriptions) contain the same kind of data as the tables in the Alleles, Insertions, Transgenic Constructs, and Aberrations tables on the gene reports, so that you can easily search for alleles or constructs with particular characteristics for several genes at a time, e.g. loss of function alleles, UAS constructs, GFP-tagged constructs.
The third file, Experimental Tool Data, complements the other two - it provides details (uses, description, compatible tools) about experimental tools (such as EGFP, mCherry, GAL4) that may be listed as components of insertional alleles or transgenic constructs in the first two files.

New Metabolic Pathway Gene Group reports

New metabolic reports include NAD(+) BIOSYNTHESIS VIA THE SALVAGE PATHWAY, TRICARBOXYLIC ACID (TCA) CYCLE, PROTEIN O-GLYCOSYLATION, PROTEIN O-GalNAcYLATION, PROTEIN O-GlcNAcYLATION, PROTEIN O-MANNOSYLATION, PROTEIN O-FUCOSYLATION, PROTEIN O-GLUCOSYLATION, PROTEIN O-GALACTOSYLATION.

New reports include MITOCHONDRIAL OXPHOS COMPLEX ASSEMBLY FACTORS, SEPTIN COMPLEXES and the SREBP-SCAP COMPLEX.

New Metabolic Pathway Reports

New metabolic reports include CHONDROITIN SULFATE PROTEOGLYCAN BIOSYNTHESIS, CHONDROITIN SULFATE PROTEOGLYCAN CATABOLISM, HEPARAN SULFATE PROTEOGLYCAN BIOSYNTHESIS, HEPARAN SULFATE PROTEOGLYCAN CATABOLISM, MALATE-ASPARTATE SHUTTLE, GLYCEROPHOSPHATE SHUTTLE, and 3’-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE (PAPS) BIOSYNTHESIS.

We have modified the search results of the ‘GAL4 etc’ Quicksearch tab to support expression pattern-based searches of Split System Combinations. The updated results table now includes an option to display results for either single alleles (including hemidrivers), or for split system combinations. For more information, see this FlyBase Tootorial or FlyBase Skeetorial.

More Stock Links

Stock reports have been added for RNAi lines from the NIG_RNAi_Fly-1 collection that are available from the National Institute of Genetics Fly Stocks (NIG-Fly). Links to the stock reports are shown in the Stocks sections of relevant report pages, including the Gene Reports.

Experimental tool updates

More sub-categories have been added to our controlled vocabulary to describe split system components, and transgenic alleles and constructs encoding these tools are now labelled with the more specific term on the appropriate reports. Examples of new sub-categories include split RNA-guided nuclease and split protease.

Updated Gene Reports for non-D. melanogaster genes

Gene Reports for non-Drosophila melanogaster genes (foreign transgenes, non-melanogaster Drosophilids, etc.) have been improved in this release. Empty sections of the Report that were not relevant for these genes have been removed, and other features have been adjusted to be more relevant for these genes.

New Macromolecular Complex & Gene Group Report Pages

Over 30 new reports have been added to the Gene Group collection, many of which are enzyme complexes and functional groups related to metabolic processes and mitochondrial function. These include the GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE COMPLEX, SERINE C-PALMITOYLTRANSFERASE COMPLEX, UDP-N-ACETYLGLUCOSAMINE TRANSFERASE COMPLEX, GAMMA-BUTYROBETAINE HYDROXYLASES, MITOCHONDRIAL TRIFUNCTIONAL PROTEIN COMPLEX and MITOCHONDRIAL DISULFIDE RELAY SYTEM.

FlyBase continues to improve our new Split System Combination reports. With this release we've added a section with details for the component alleles contributing to the combination. The section shows a free text description for each allele, as well as a table listing the encoded driver/tool, and any regulatory region, inserted elements or tags.

New Macromolecular Complex groups

New Macromolecular Complex groups have been added including the MITOCHONDRIAL IRON-SULFUR ASSEMBLY COMPLEX, MITOCHONDRIAL DNA REPLISOME, MTV COMPLEX, and IRM ADHESION COMPLEXES.

Bulk data best practices

Do you use scripts written with Python or other languages to "scrape" data from FlyBase pages? Did you know that such scripts can cause service interruptions for other users, or worse? Scripts can be written so that they are much less likely to create such problems, and alternatives to scripts may better meet your data needs. If you or your work colleagues use scripts, please read our Commentary on Best practices for getting bulk data from FlyBase.

The new Gene ToolKit section in Gene Reports displays a set of key genetic reagents that can be used to study a gene of interest. Categories shown include loss of function allele, UAS RNAi transgene, UAS wild-type cDNA, genomic rescue transgene. For each category, the most commonly used reagent, based on frequency of usage in research papers and stock availability, is shown, along with a link to any publicly available stocks. To view all the reagents for a particular category, click the See All button. For more details see this commentary.

Experimental tool updates

• New reporter enzyme sub-categories
  Two sub-categories have been introduced for reporter enzymes - bioluminescence reporter and chemical labeling reporter. Transgenic alleles and constructs encoding these type of reporter enzymes are now labelled with the more specific term on the appropriate reports. Examples of bioluminescence reporter include pLUC, NanoLuc. Examples of chemical labeling reporter include SNAPf-tag, Halo7-tag.

• ‘deGrad’ tool reports
  Experimental Tool Reports have been made for the deGradFP and deGradHA tools, which can be used to target GFP-tagged and HA-tagged proteins respectively for degradation, to make it easier to find transgenes encoding these tools.

New Macromolecular Complex Report Pages

We are introducing a new way to find macromolecular complexes. FlyBase Macromolecular Complex Reports are available for 254 complexes and can be searched via new QuickSearch tab on our homepage or browsed separately via a Macromolecular Complex Report List. For more details see this commentary.

Multiple term filtering added to the Alleles and Transgenic Construct tables on the gene reports

Many of the columns in the tables of the Alleles, Insertions, Constructs, and Aberrations section of the Gene Report now support filtering using multiple terms; these can be identified by the [+] icon at the bottom right of the Filter box at the top of the column. Filtering for a single term works as before; simply start typing in the Filter box and the column is filtered for matching entries as you type. To add a second term to the filtering, ‘store’ the first term either by hitting return or the [+] icon at the bottom right of the Filter box; the ‘stored’ term will appear in light blue at the top of the Filter box. Then continue typing to add the second filter term; the column is filtered for entries that contain both terms. For example, searching for both “GFP” and “HA” in the Tagged with column of the Transgenic Construct table will identify any matching doubly-tagged transgenes for that gene.

More images in the Frequently Used GAL4 Drivers resource

We have added another 150 new images, illustrating GAL4 expression patterns, to the Frequently Used GAL4 Drivers table. This resource currently consists of 337 GAL4 alleles, which include the 150 drivers most frequently ordered from the Bloomington Drosophila Stock Center and/or those used in at least 20 publications. With this update, over 90% now have representative images. All images were collected from publications distributed using the Creative Commons Attribution License, or that were published in journals that have granted FlyBase permission to use. The link to the Frequently Used GAL4 Drivers Table can be found at the bottom of the “GAL4 etc” QuickSearch tab. If you’d like to contribute an image for one the remaining 19 non-ubiquitously expressed GAL4 drivers, please let us know via the dedicated “Contact FlyBase” button on the Frequently Used GAL4 Drivers Table page.

Testis-specificity index

We have added the testis-specificity index score from Vedelek et al. (2018) to the Expression section of the Gene Report. The index, calculated from modENCODE data, indicates the degree of testis expression bias and ranges from -2.52 (underrepresented) to 5.2 (very high testis bias). The degree of testis expression bias may be particularly useful when comparing paralogs. For example, the SdhAL paralog of SdhA, has a testis-specificity index of 5.16 compared with 1.34 of the more ubiquitously expressed SdhA. The values for each gene can be found in the High-Throughput Gene Expression bulk download file.

Gene counts added to Gene Group, Pathway and Complex lists

The number of member genes for each group is now visible on the browsable report lists for Gene Groups, Macromolecular Complexes and Pathways.

We have added report pages for ‘split system combinations’, where two hemidrivers are brought together, resulting in a functional driver being expressed in a restricted expression pattern that corresponds to the intersection of the expression patterns of the hemidrivers.
The new combination reports (e.g. Scer\GAL4^DBD.R22B12∩Hsap\RELA^AD.R14E06, Scer\GAL4^DBD.R72B05∩Hsap\RELA^AD.ple) currently include the FBco identifier, synonyms, the transgenic hemidriver alleles that make up the combination, expression pattern data and links to stocks corresponding to the combination.
The combination pages have been added to hitlists, so if you search for a regulatory region that drives expression of one of the hemidrivers in a combination (e.g. R72B05, VT064569, ple) you will see the relevant combination(s) in the hitlist. These new report pages will get improvements during the coming months, including images of expression patterns when available.

Transmembrane Transporter Collection

Transmembrane transport allows the passage of solutes and molecules across lipid bilayers. Transmembrane transporters encompass a wide variety of protein assemblies, mechanisms and systems, from pore-forming subunits that allow the passive diffusion of solutes to complex molecular machines such as ATP synthase, or systems such as the mitochondrial protein transport system.
To enable users to more easily find Drosophila melanogaster genes involved in transmembrane transport, we have collated a list of genes encoding transmembrane transporters and integrated them into the FlyBase Gene Groups resource. The TRANSMEMBRANE TRANSPORTERS are divided into four major classes: CHANNELS AND PORES, PRIMARY ACTIVE TRANSPORTERS, PROTEIN TRANSLOCASES, DISLOCASES AND MEMBRANE INSERTASES and the SOLUTE CARRIER FAMILY.
TRANSMEMBRANE TRANSPORTERS have been assembled using multiple sources, including data from Gene Ontology (GO) annotation, the Transporter Classification Database and publications. In concert with building this resource, GO annotation has been reviewed and updated to be more accurate and to provide better coverage. In total, 1112 genes have been assembled into 229 transporter sub-groups based on functional and sequence features.
We believe this to be the most comprehensive resource for Drosophila melanogaster transmembrane transporters and we welcome feedback from the community to help improve its accuracy and utility.

Linkouts to KEGG and Reactome pathways updated

We have refreshed the links between FlyBase genes and KEGG and Reactome pathways. These links are displayed in the Pathways section of FlyBase gene reports and display the name of the KEGG/Reactome pathway(s) associated with the given gene at those databases. Note that links to KEGG/Reactome metabolic pathways are specifically displayed in the Pathways → Metabolic Pathways subsection of the gene report, alongside similar links to FlyCyc. For example, see the reports for Egfr or Gapdh1.

Link to FlyPredictome

FlyPredictome offers computationally predicted protein-protein interactions through AlphaFold-Multimer. This new platform enriches the analysis of protein complexes by providing measures of interaction strength and contact area, based on the predicted aligned error (PAE). These metrics enhance the detection of direct interactions, advancing computational approaches in PPI network identification. Find a link to this new service under Tool/Reagent Resources in the FlyBase home page sidebar.

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