FlyBase: genes and gene models

By Rachel A. Drysdale, Madeline A. Crosby. Nucleic Acids Res., 2004

399 citations recorded by the source corpus.

FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosphila species.

Subfields: Insect Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a6a0df4a95cba3dff90ff8b65843ed1b942d01f4

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Citations in the corpus

TreeFam: a curated database of phylogenetic trees of animal gene families (2005, methodology): “To curate a tree, the curator gathers phylogenetic and functional information on the genes in the family from journal articles; from manually curated databases such as UniProt (18), FlyBase ( 28 ), WormBase”
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes (2005, background): “Often called model organism databases, or organism-specific databases, examples include EcoCyc for Escherichia coli (1), PseudoCyc for Pseudomonas aeruginosa (2), PlasmoCyc for Plasmodium falciparum (3), SGD for Saccharomyces cerevisiae (4), TAIR for Arabidopsis thaliana (5), MGD for Mus musculus (m”
Normal microRNA Maturation and Germ-Line Stem Cell Maintenance Requires Loquacious, a Double-Stranded RNA-Binding Domain Protein (2005, neutral): “genome sequencing project and annotated in FlyBase [”
TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes (2005, background): “In addition, the Drosophila gene entries linked to the newly imported sites contain pointers to FlyBase (24) and EntrezGene (17).”
Creating a honey bee consensus gene set (2007, methodology): “When genes are manually analyzed, a more definitive and comprehensive gene list can be provided for use by all users, for example the Drosophila melanogaster gene list at FlyBase [3, 4 ].”
BioGRID: a general repository for interaction datasets (2005, background): “The BioGRID is actively linked to the Saccharomyces Genome Database (30), Flybase (27) and Germ Online (31) websites.”
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development (2011, methodology): “Likewise, the DDE density was calculated for each TSS in the genome [61].”
Daphnia as an emerging model for toxicological genomics (2008, background): “These results suggest that the elaborate functional genetic database for the fruitfly (Drysdale et al., 2005) may be a valuable resource for making predictions about the biological function for a majority of Daphnia genes.”
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology (2010, background): “Development of organism-specific DBs Organism-specific DBs (also known as MODs) describe the genome and other information about an organism [8–19].”
The UCSC Genome Browser Database: update 2006 (2005, background): “Several gene tracks are imported from major model organism databases: FlyBase (38) genes for D.”
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes (2013, methodology): “Phenotype and disease data from SGD [ 77 ] , MGI [ 78 ] , Wormbase [ 79 ] , Flybase [ 80 ] , GSEA [ 20 ] , Zfin [ 81 ] were incorporated into our functional networks by summing the co - occurrences of gene pairs in all phenotypes / diseases and normalizing by the size of the phenotype / disease .”
Biomedical ontologies: a functional perspective (2007, background): “Many groups are creating ontologies, from biologists and bench researchers [6–8] to clinical researchers and clinical practitioners [9–12].”