FlyBase 101 – the basics of navigating FlyBase

By Peter McQuilton, Susan E. St. Pierre, Jim Thurmond. Nucleic Acids Res., 2011

394 citations recorded by the source corpus.

FlyBase (http://flybase.org) is the leading database and web portal for genetic and genomic information on the fruit fly Drosophila melanogaster and related fly species. Whether you use the fruit fly as an experimental system or want to apply Drosophila biological knowledge to another field of study, FlyBase can help you successfully navigate the wealth of available Drosophila data. Here, we review the FlyBase web site with novice and less-experienced users of FlyBase in mind and point out recent developments stemming from the availability of genome-wide data from the modENCODE project. The first section of this paper explains the organization of the web site and describes the report pages available on FlyBase, focusing on the most popular, the Gene Report. The next section introduces some of the search tools available on FlyBase, in particular, our heavily used and recently redesigned search tool QuickSearch, found on the FlyBase homepage. The final section concerns genomic data, including recent modENCODE (http://www.modencode.org) data, available through our Genome Browser, GBrowse.

Subfields: Insect Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9188456cdc1bcd9cafaf7146170368cff0ab3b6b

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Insect Science

In Molecular Biology

Citations in the corpus

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, positive): “We used bowtie (29) to map single-‐ and paired-‐end Illumina sequencing data to the Drosophila genome (dm3), excluding chromosomes U, Uextra, and the mitochondrial genome or the human genome (hg19), only cons”
FlyBase 102—advanced approaches to interrogating FlyBase (2013, methodology): “More detailed information about how to navigate the homepage and how to use QuickSearch and GBrowse are covered in a previous paper (6).”
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines (2014, background): “myotubularin (mtm), which is involved in chromosome segregation and the mitotic cell cycle (McQuilton et al. 2012), is a plausible candidate gene associated with genome size and reached Bonferroni-level significance in the gene-based tests of association with this trait.”
Spatial expression of transcription factors in Drosophila embryonic organ development (2013, background): “Columns A-D show the FlyBase identifiers, gene symbols, and synonyms for the 708 TF genes described in this study and their associated DNA binding domains (DBD).”
The BioGRID interaction database: 2013 update (2012, background): “Collaborations are also underway with WormBase (23), ZFIN (25), FlyBase (26), MGI (27) and CGD (28) to coordinate interaction curation, and thereby leverage expertise and in-house MOD data that are relevant to biological interactions.”
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs (2012, methodology): “OrthoDB gene annotations are enhanced with detailed functional data from well-studied model organisms in each lineage to highlight phenotypes associated with genes from Mus musculus, Drosophila melanogaster and Saccharomyces cerevisiae, sourced from the Mouse Genome Database (47), FlyBase (30) and S”
COMPARTMENTS: unification and visualization of protein subcellular localization evidence (2014, methodology): “The first channel, called knowledge, is based on annotations from UniProtKB (1), MGI (2), SGD (3), FlyBase (4) and WormBase (5).”
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm (2014, methodology): “The annotated euchromatin portion of the D. melanogaster genome (14) was downloaded from FlyBase (15).”