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BMC Bioinformatics. 2019 May 17;20(1):255. doi: 10.1186/s12859-019-2805-6.

Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration.

Author information

1
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
2
Present address: Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA.
3
Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA.
4
Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA.
5
Superfund Research Center, Oregon State University, Corvallis, OR, USA.
6
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. katrina.waters@pnnl.gov.
7
Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. katrina.waters@pnnl.gov.
8
Superfund Research Center, Oregon State University, Corvallis, OR, USA. katrina.waters@pnnl.gov.
9
Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. susan.tilton@oregonstate.edu.
10
Superfund Research Center, Oregon State University, Corvallis, OR, USA. susan.tilton@oregonstate.edu.

Abstract

BACKGROUND:

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. 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.

RESULTS:

BRM 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.

CONCLUSIONS:

Overall, 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/ .

KEYWORDS:

Bioinformatics; Genomics; MicroRNA; Systems biology; Zebrafish

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