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Title: Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration

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 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 RNAseq 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 toolsmore » 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/.« less

Authors:
ORCiD logo [1];  [1];  [1];  [2];  [2];  [2];  [1]; ORCiD logo [1];  [2]
  1. BATTELLE (PACIFIC NW LAB)
  2. Oregon State University
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1525323
Report Number(s):
PNNL-SA-138423
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
BMC Bioinformatics
Additional Journal Information:
Journal Volume: 20
Country of Publication:
United States
Language:
English
Subject:
bioinformatics, MicroRNA, systems biology, Genomics, zebrafish

Citation Formats

Brown, Joseph M., Phillips, Aaron R., Lewis, David A., Mans, Michael-Andres, Chang, Yvonne, Tanguay, Robert, Peterson, Elena S., Waters, Katrina M., and Tilton, Susan C. Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration. United States: N. p., 2019. Web. doi:10.1186/s12859-019-2805-6.
Brown, Joseph M., Phillips, Aaron R., Lewis, David A., Mans, Michael-Andres, Chang, Yvonne, Tanguay, Robert, Peterson, Elena S., Waters, Katrina M., & Tilton, Susan C. Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration. United States. doi:10.1186/s12859-019-2805-6.
Brown, Joseph M., Phillips, Aaron R., Lewis, David A., Mans, Michael-Andres, Chang, Yvonne, Tanguay, Robert, Peterson, Elena S., Waters, Katrina M., and Tilton, Susan C. Fri . "Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration". United States. doi:10.1186/s12859-019-2805-6.
@article{osti_1525323,
title = {Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration},
author = {Brown, Joseph M. and Phillips, Aaron R. and Lewis, David A. and Mans, Michael-Andres and Chang, Yvonne and Tanguay, Robert and Peterson, Elena S. and Waters, Katrina M. and Tilton, Susan C.},
abstractNote = {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 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 RNAseq 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/.},
doi = {10.1186/s12859-019-2805-6},
journal = {BMC Bioinformatics},
number = ,
volume = 20,
place = {United States},
year = {2019},
month = {5}
}

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