Abstract
BackgroundThe Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. In addition to providing a robust means of identifier conversion, BRM also incorporates a suite of microRNA (miRNA)-target databases upon which to query target genes or to perform reverse target lookups using gene identifiers.ResultsBRM has the capability to perform cross-species identifier lookups across common identifier types, directly integrate datasets across platform or species by performing identifier retrievals in the background, and retrieve miRNA targets from multiple databases simultaneously and integrate the resulting gene targets with experimental mRNA data. Here we use workflows provided in BRM to integrate RNA sequencing data across species to identify common biomarkers of exposure after treatment of human lung cells and zebrafish to benzo[a]pyrene (BAP). We further use the miRNA Target workflow to experimentally determine the role of miRNAs as regulators of BAP toxicity and identify the predicted functional consequences of miRNA-target regulation in our system. The output from BRM can easily and directly be uploaded to freely available visualization tools for further analysis. From these examples, we were able to identify an important role for several miRNAs as potential regulators of BAP toxicity in human lung cells associated with cell migration, cell communication, cell junction assembly and regulation of cell death.ConclusionsOverall, BRM provides bioinformatics tools to assist biologists having minimal programming skills with analysis and integration of high-content omics’ data from various transcriptomic and proteomic platforms. BRM workflows were developed in Java and other open-source technologies and are served publicly using Apache Tomcat at https://cbb.pnnl.gov/brm/.
Highlights
IntroductionThe Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species
The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, and Macaca mulatta, as well as perform orthologous conversions among the supported species
Cross-species data integration Here we present an example in which global transcriptomics analyses from two species are integrated in BRM to identify the subset of genes regulated in common after exposure of zebrafish embryos and human bronchial epithelial cells (HBEC) exposed to benzo[a]pyrene (BAP) for 48 h
Summary
The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. BioMart [2] integrates internal and external data to convert identifiers and provide orthologous gene information for model organisms The functionality of these web-based conversion tools, like BRM, relies on user provided gene lists, DAVID and BioMart lack the ability to merge identifier conversions with existing datasets. BRM allows users to integrate data tables based on (1) string matching for tables that include common identifier types or (2) identifier conversion using National Center for Biotechnology Information (NCBI), Uniprot and Ensembl databases to allow for integration of tables without common identifier types (e.g. cross-species integration, gene-to-protein integration) Other tools, such as GeneWeaver, allow for identifier mapping within the context of their data analysis pipeline and tools for functional genomics [3]. While BRM will perform these functions within the context of BRM workflows, it allows users to update their omics tables with new metadata and biomolecular identifiers for use in any data analysis or software programs of interest
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