FlyBase: establishing a Gene Group resource for Drosophila melanogaster

By H. Attrill, Kathleen Falls, J. Goodman, G. Millburn, Giulia Antonazzo, Alix J. Rey, Steven J. Marygold. Nucleic Acids Res., 2015

327 citations recorded by the source corpus.

Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify genes related in sequence; high-throughput genetic and molecular screens reveal functionally related gene products; and advanced proteomic methods can determine the subunit composition of multi-protein complexes. It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so that researchers can readily access these data alongside other relevant information. To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a ‘Gene Group’ resource: high-quality sets of genes derived from the published literature and organized into individual report pages. To facilitate further analyses, Gene Group Reports also include convenient download and analysis options, together with links to equivalent gene groups at other databases. This new resource will enable researchers with diverse backgrounds and interests to easily view and analyse acknowledged D. melanogaster gene sets and compare them with those of other species.

Subfields: Insect Science, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/0d58fdc5f1dfcb2910f7cc003338a82ef827f85c

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Citations in the corpus

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse (2016, background): “In 2016, MGD joined FlyBase (15), Saccharomyces Genome Database (SGD) (16), WormBase (17), Zebrafish Information Network (ZFIN) (18), Rat Genome Database (RGD) (19) and the Gene Ontology Consortium (GOC) to form the Alliance of Genome Resources D ow naded rom http/academ ic.”
FlyBase 2.0: the next generation (2018, background): “0, this includes a Gene Snapshot, an automatically generated summary, the description of the Gene Group to which the gene belongs (3), UniProt function data, historical Red Book information (4), and a summary from Interactive Fly (http://www.”
Lepbase: the Lepidopteran genome database (2016, background): “All results and datafiles are available at http://download.lepase.org”
FlyBase at 25: looking to the future (2016, methodology): “Recent years have seen the addition of Gene Group Reports (1), the design of multiple tools to access RNA-Seq data, improvements to FlyBase ontologies (15,16), the incorporation of the Disease Ontology (17,18), the addition of the user–curation tool Fast-Track Your Paper (19) and enhancements to our”
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016, background): “The break in the bottom left of Chromosome 2L could not be confidently identified but is next to a feature labeled “ FlyBase transposable element ” in the genome annotation and is likely a transposable element insertion site.”