FlyBase: Integration and improvements to query tools

Department of Biology, Indiana University 1001 E 3rd Street, Bloomington, IN 47405, USA.
Nucleic Acids Research (Impact Factor: 9.11). 02/2008; 36(Database issue):D588-93. DOI: 10.1093/nar/gkm930
Source: PubMed


FlyBase ( is the primary resource for molecular and genetic information on the Drosophilidae. The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide
efficient access to the data available and facilitate the discovery of significant relationships within the database. Recently,
FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to
the search tools QuickSearch and QueryBuilder. Furthermore, these search tools have been integrated with Batch Download and
new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.

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    • "A P-value was estimated from the number of random protein sets with mean ERC values equal to or greater than the mean ERC between Shu complex proteins. Sets of mitotic, meiotic, and " recombinase activity " proteins were obtained from the Gene Ontology Annotation Database through the Yeast Mine and FlyBase Query Builder web tools for yeast and Drosophila, respectively (Wilson et al. 2008; Balakrishnan et al. 2012). Statistical significance for ERC between Shu2 and these functional groups was determined by comparing their ERC distributions with the whole-proteome background (all genes) through Wilcoxon rank-sum tests. "
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    ABSTRACT: The Saccharomyces cerevisiae Shu2 protein is an important regulator of Rad51 that promotes homologous recombination (HR). Shu2 functions in the Shu complex with Shu1 and the Rad51 paralogs Csm2 and Psy3. Shu2 belongs to the SWS1 protein family, which is characterized by its SWIM domain (CXC...Xn...CXH), a zinc binding motif. In humans SWS1 interacts with the RAD51 paralog SWSAP1. Using genetic and evolutionary analyses, we examined the role of the Shu complex in mitotic and meiotic processes across eukaryotic lineages. We provide evidence that the SWS1 protein family contains orthologous genes in early-branching eukaryote lineages (e.g. Giardia lamblia), as well as in multi-cellular eukaryotes including Caenorhabditis elegans and Drosophila melanogaster. Using sequence analysis, we expand the SWIM domain to include an invariant alanine three residues after the terminal CXH motif (CXC...Xn...CXHXXA). We find the SWIM domain is conserved in all eukaryotic orthologs, and accordingly, in vivo disruption of the invariant residues within the canonical SWIM domain inhibits DNA damage tolerance in yeast and protein-protein interactions in yeast and humans. Furthermore, using evolutionary analyses we find that yeast and Drosophila Shu2 exhibit strong co-evolutionary signatures with meiotic proteins, and in yeast its disruption leads to decreased meiotic progeny. Together, our data indicate that the SWS1 family is an ancient and highly conserved eukaryotic regulator of meiotic and mitotic HR. Copyright © 2015, The Genetics Society of America.
    Full-text · Article · Feb 2015 · Genetics
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    • "Curation of information by experts helps to ensure quality. Methods for querying data in FlyBase have recently been presented elsewhere (Wilson et al. 2008; McQuilton et al. 2012; St Pierre et al. 2014). The National Center for Biotechnology Information (NCBI) gene database ( "
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    ABSTRACT: Drosophila melanogaster has become a system-of-choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents, or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, 'meta' information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved, and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally.
    Full-text · Article · Mar 2014 · Genetics
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    • "These bands were reduced in lysate from the P-element containing allele lqfR03685 and appeared to be absent in lysate from mutant lqfRD66 (see below). The bands were also not recognized by pre-immune serum (data not shown) indicating that these bands represent LqfR proteins, although both are larger than the 69 kDa and 158 kDa expected sizes of the products of the 2.7 kb and 5 kb isoforms [20]. However, reduced mobility is consistent with what has been seen with other ENTH domain-containing proteins, including epsin and CLINT1 in vertebrates [9], [21] and EPSIN1 (which is functionally like CLINT1) in Arabidopsis thaliana [12]. "
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    ABSTRACT: Clathrin interactor 1 [CLINT1] (also called enthoprotin/EpsinR) is an Epsin N-terminal homology (ENTH) domain-containing adaptor protein that functions in anterograde and retrograde clathrin-mediated trafficking between the trans-Golgi network and the endosome. Removal of both Saccharomyces cerevisiae homologs, Ent3p and Ent5p, result in yeast that are viable, but that display a cold-sensitive growth phenotype and mistrafficking of various vacuolar proteins. Similarly, either knock-down or overexpression of vertebrate CLINT1 in cell culture causes mistrafficking of proteins. Here, we have characterized Drosophila CLINT1, liquid-facets Related (lqfR). LqfR is ubiquitously expressed throughout development and is localized to the Golgi and endosome. Strong hypomorphic mutants generated by imprecise P-element excision exhibit extra macrochaetae, rough eyes and are female sterile. Although essentially no eggs are laid, the ovaries do contain late-stage egg chambers that exhibit abnormal morphology. Germline clones reveal that LqfR expression in the somatic follicle cells is sufficient to rescue the oogenesis defects. Clones of mutant lqfR follicle cells have a decreased cell size consistent with a downregulation of Akt1. We find that while total Akt1 levels are increased there is also a significant decrease in activated phosphorylated Akt1. Taken together, these results show that LqfR function is required to regulate follicle cell size and signaling during Drosophila oogenesis.
    Preview · Article · Oct 2011 · PLoS ONE
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