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ArrayTrack: An FDA and Public Genomic Tool

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Biological Networks and Pathway Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1613))

Abstract

A robust bioinformatics capability is widely acknowledged as central to realizing the promises of toxicogenomics. Successful application of toxicogenomic approaches, such as DNA microarrays, inextricably relies on appropriate data management, the ability to extract knowledge from massive amounts of data and the availability of functional information for data interpretation. At the FDA’s National Center for Toxicological Research (NCTR), we are developing a public microarray data management and analysis software, called ArrayTrack that is also used in the routine review of genomic data submitted to the FDA. ArrayTrack stores a full range of information related to DNA microarrays and clinical and nonclinical studies as well as the digested data derived from proteomics and metabonomics experiments. In addition, ArrayTrack provides a rich collection of functional information about genes, proteins, and pathways drawn from various public biological databases for facilitating data interpretation. Many data analysis and visualization tools are available with ArrayTrack for individual platform data analysis, multiple omics data integration and integrated analysis of omics data with study data. Importantly, gene expression data, functional information, and analysis methods are fully integrated so that the data analysis and interpretation process is simplified and enhanced. Using ArrayTrack, users can select an analysis method from the ArrayTrack tool box, apply the method to selected microarray data and the analysis results can be directly linked to individual gene, pathway, and Gene Ontology analysis. ArrayTrack is publicly available online (http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm), and the prospective user can also request a local installation version by contacting the authors.

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Abbreviations

CDISC:

Clinical Data Interchange Standard Consortium

DEG:

Differentially Expressed Gene

FDA:

Food and Drug Administration

GO:

Gene Ontology

GOFFA:

Gene Ontology For Functional Analysis

HCA:

Hierarchical Cluster Analysis

IPA:

Ingenuity Pathway Analysis

KEGG:

Kyoto Encyclopedia of Genes and Genomes

MAQC:

MicroArray Quality Control

MIAME:

Minimum Information About a Microarray Experiment

NCTR:

National Center for Toxicological Research

PCA:

Principal Component Analysis

PGx:

Pharmacogenomics

SDTM:

Study Data Tabulation Model

TGx:

Toxicogenomics

VGDS:

Voluntary Genomic Data Submission

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Author information

Authors and Affiliations

  1. Z-Tech Corporation, An ICF International Company, 3900 NCTR Road, Jefferson, AR, 72079, USA

    Hong Fang, Feng Qian & Roger Perkins

  2. Division of Systems Toxicology, National Center for Toxicological Research (NCTR), FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA

    Stephen C. Harris, Zhenjiang Su, Minjun Chen, Leming Shi & Weida Tong

Authors
  1. Hong Fang
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  2. Stephen C. Harris
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  3. Zhenjiang Su
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  4. Minjun Chen
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  5. Feng Qian
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  6. Leming Shi
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  7. Roger Perkins
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  8. Weida Tong
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Corresponding author

Correspondence to Weida Tong .

Editor information

Editors and Affiliations

  1. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Tatiana V. Tatarinova

  2. Prosapia Genetics, Solana Beach, California, USA

    Yuri Nikolsky

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Fang, H. et al. (2017). ArrayTrack: An FDA and Public Genomic Tool. In: Tatarinova, T., Nikolsky, Y. (eds) Biological Networks and Pathway Analysis. Methods in Molecular Biology, vol 1613. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7027-8_13

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  • DOI: https://doi.org/10.1007/978-1-4939-7027-8_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7025-4

  • Online ISBN: 978-1-4939-7027-8

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