FlyMine: an integrated database for Drosophila and Anopheles genomics

Abstract

FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists. RationaleWith the completion of increasing numbers of genome sequences has come an explosion in the development of both computational and experimental techniques for deciphering the functions of genes, molecules and their interactions. These include theoretical methods for deducing function, such as analysis of protein homologies, structural domain predictions, phylogenetic profiling and analysis of protein domain fusions, as well as experimental techniques, such as microarray-based gene expression and transcription factor binding studies, two-hybrid protein-protein interaction screens, and large-scale RNA interference (RNAi) screens. The result is a huge amount of information and a current challenge is to extract meaningful knowledge and patterns of biological significance that can lead to new experimentally testable hypotheses. Many of these broad datasets, however, are noisy and the data quality can vary significantly. While in some circumstances the data from each of these techniques are useful in their own right, the ability to combine data from different sources facilitates interpretation and potentially allows stronger inferences to be made. Currently, biological data are stored in a wide variety of formats in numerous different places, making their combined analysis difficult: when information from several different databases is required, the assembly of data into a format suitable for querying is a challenge in itself. Sophisticated analysis of diverse data requires that they are available in a form that allows questions to be asked across them and that tools for constructing the questions are available. The development of systems for the integration and combined analysis of diverse data remains a priority in bioinformatics. Avoiding the need to understand and reformat many different data sources is a major benefit for end users of a centralized data access system.A number of studies have illustrated the power of integrating data for cross-validation, functional annotation and generating testable hypotheses (reviewed in [1,2]). These studies have covered a range of data types; some looking at the overlap between two different data sets, for example, protein interaction and expression data [3][4][5][6] Another key component is the use of ontologies that provide a standardized system for naming biological entities and their relationships and this aspect is based on the approach taken by the Chado schema [28]. For example, a large part of the FlyMine data model is based on the Sequence Ontology (a controlled-vocabulary for describing biological sequences) [29...

High Intake of Dietary Sugar Enhances Bisphenol A (BPA) Disruption and Reveals Ribosome-Mediated Pathways of Toxicity

“…Significance was calculated with standard Fisher's exact tests on contingency tables with counts of genes displaying differential expression. Analyses of enrichment in gene ontology categories were performed with standard methods as previously implemented (Branco et al 2013) and confirmed with the FlyMine platform (Lyne et al 2007). …”

Reproductive activity triggers accelerated male mortality and decreases lifespan: genetic and gene expression determinants in Drosophila

“…Tissue specificity of differentially expressed genes was assessed as previously described (Branco et al, 2013) using the FlyAtlas resource (Chintapalli et al, 2007). Discovery of gene ontology enrichments were done with the FlyMine platform and enrichment P-values corrected with Holm-Bonferroni (Lyne et al, 2007).…”

Gene Duplication, Lineage-Specific Expansion, and Subfunctionalization in the MADF-BESS Family Patterns theDrosophilaWing Hinge

“…The number of MADF, BESS, and MADF-BESS domains were counted in different species in the animal kingdom based on information available in databases such as InterPro (Hunter et al 2012), UniProt (Magrane and Consortium 2011), Flybase (Marygold et al 2013), Flymine (Lyne et al 2007), SMART (Schultz et al 1998), 12 Drosophila genomes (Clark et al 2007), and ORTHODB (Waterhouse et al 2013). MADF-BESS domain protein sequences were downloaded from UniProt.…”