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Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an ‘omics’ study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.

 

FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information aboutDrosophila melanogaster. The long and rich history ofDrosophilaresearch, combined with recent surges in genomic‐scale and high‐throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Using the “Search FlyBase” tab of QuickSearch

Basic Protocol 2: Using the “Data Class” tab of QuickSearch

Basic Protocol 3: Using the “References” tab of QuickSearch

Basic Protocol 4: Using the “Gene Groups” tab of QuickSearch

Basic Protocol 5: Using the “Pathways” tab of QuickSearch

Basic Protocol 6: Using the “GO” tab of QuickSearch

Basic Protocol 7: Using the “Protein Domains” tab of QuickSearch

Basic Protocol 8: Using the “Expression” tab of QuickSearch

Basic Protocol 9: Using the “GAL4 etc” tab of QuickSearch

Basic Protocol 10: Using the “Phenotype” tab of QuickSearch

Basic Protocol 11: Using the “Human Disease” tab of QuickSearch

Basic Protocol 12: Using the “Homologs” tab of QuickSearch

Support Protocol 1: Managing FlyBase hit lists

 

FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.

 

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO—a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations—evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)—mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

 

Transfer RNAs (tRNAs) are ubiquitous adapter molecules that link specific codons in messenger RNA (mRNA) with their corresponding amino acids during protein synthesis. The tRNA genes of Drosophila have been investigated for over half a century but have lacked systematic identification and nomenclature. Here, we review and integrate data within FlyBase and the Genomic tRNA Database (GtRNAdb) to identify the full complement of tRNA genes in the D. melanogaster nuclear and mitochondrial genomes. We apply a logical and informative nomenclature to all tRNA genes, and provide an overview of their characteristics and genomic features. 

Abstract The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides. 

UDP-glycosyltransferases (UGTs) are important conjugation enzymes found in all kingdoms of life, catalyzing a sugar conjugation with small lipophilic compounds and playing a crucial role in detoxification and homeostasis. The UGT gene family is defined by a signature motif in the C-terminal domain where the uridine diphosphate (UDP)-sugar donor binds. UGTs have been identified in a number of insect genomes over the last decade and much progress has been achieved in characterizing their expression patterns and molecular functions. Here, we present an update of the complete repertoire of UGT genes in Drosophila melanogaster and provide a brief overview of the latest research in this model insect. A total of 35 UGT genes are found in the D. melanogaster genome, localized to chromosomes 2 and 3 with a high degree of gene duplications on the chromosome arm 3R. All D. melanogaster UGT genes have now been named in FlyBase according to the unified UGT nomenclature guidelines. A phylogenetic analysis of UGT genes shows lineage-specific gene duplications. Analysis of anatomical and induced gene expression patterns demonstrate that some UGT genes are differentially expressed in various tissues or after environmental treatments. Extended searches of UGT orthologs from 18 additional Drosophila species reveal a diversity of UGT gene numbers and composition. The roles of Drosophila UGTs identified to date are briefly reviewed, and include xenobiotic metabolism, nicotine resistance, olfaction, cold tolerance, sclerotization, pigmentation, and immunity. Together, the updated genomic information and research overview provided herein will aid further research in this developing field. 

UDP-glycosyltransferases (UGTs) are important conjugation enzymes found in all kingdoms of life, catalyzing a sugar conjugation with small lipophilic compounds and playing a crucial role in detoxification and homeostasis. The UGT gene family is defined by a signature motif in the C-terminal domain where the uridine diphosphate (UDP)-sugar donor binds. UGTs have been identified in a number of insect genomes over the last decade and much progress has been achieved in characterizing their expression patterns and molecular functions. Here, we present an update of the complete repertoire of UGT genes in Drosophila melanogaster and provide a brief overview of the latest research in this model insect. A total of 35 UGT genes are found in the D. melanogaster genome, localized to chromosomes 2 and 3 with a high degree of gene duplications on the chromosome arm 3R. All D. melanogaster UGT genes have now been named in FlyBase according to the unified UGT nomenclature guidelines. A phylogenetic analysis of UGT genes shows lineage-specific gene duplications. Analysis of anatomical and induced gene expression patterns demonstrate that some UGT genes are differentially expressed in various tissues or after environmental treatments. Extended searches of UGT orthologs from 18 additional Drosophila species reveal a diversity of UGT gene numbers and composition. The roles of Drosophila UGTs identified to date are briefly reviewed, and include xenobiotic metabolism, nicotine resistance, olfaction, cold tolerance, sclerotization, pigmentation, and immunity. Together, the updated genomic information and research overview provided herein will aid further research in this developing field. 

The neprilysin (M13) family of metalloendopeptidases comprises highly conserved ectoenzymes that cleave and thereby inactivate many physiologically relevant peptides in the extracellular space. Impaired neprilysin activity is associated with numerous human diseases. Here, we present a comprehensive list and classification of M13 family members in Drosophila melanogaster. Seven Neprilysin (Nep) genes encode active peptidases, while 21 Neprilysin-like (Nepl) genes encode proteins predicted to be catalytically inactive. RNAseq data demonstrate that all 28 genes are expressed during development, often in a tissue-specific pattern. Most Nep proteins possess a transmembrane domain, whereas almost all Nepl proteins are predicted to be secreted. 

With the advent of single-cell RNA sequencing (scRNA-seq) technologies, there has been a spike in stud-ies involving scRNA-seq of several tissues across diverse species includingDrosophila. Although a fewdatabases exist for users to query genes of interest within the scRNA-seq studies, search tools that enableusers to find orthologous genes and their cell type-specific expression patterns across species are limited.Here, we built a new search database, DRscDB (https://www.flyrnai.org/tools/single_cell/web/), toaddress this need. DRscDB serves as a comprehensive repository for published scRNA-seq datasets forDrosophilaand relevant datasets from human and other model organisms. DRscDB is based on manualcuration ofDrosophilascRNA-seq studies of various tissue types and their corresponding analogoustissues in vertebrates including zebrafish, mouse, and human. Of note, our search database provides mostof the literature-derived marker genes, thus preserving the original analysis of the published scRNA-seqdatasets. Finally, DRscDB serves as a web-based user interface that allows users to mine gene expressiondata from scRNA-seq studies and perform cell cluster enrichment analyses pertaining to variousscRNA-seq studies, both within and across species.