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ArrayTrack: An FDA and Public Genomic Tool

  • Hong Fang
  • Stephen C. Harris
  • Zhenjiang Su
  • Minjun Chen
  • Feng Qian
  • Leming Shi
  • Roger Perkins
  • Weida TongEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

ArrayTrack Bioinformatics MAQC Pharmacogenomics VXDS VGDS Microarray Toxicogenomics Systems Toxicology Database Genomics 

Abbreviation

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

References

  1. 1.
    Schmidt CW (2002) Toxicogenomics: an emerging discipline. Environ Health Perspect 110:A750–A755CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Afshari CA, Nuwaysir EF, Barrett JC (1999) Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. Cancer Res 59:4759–4760PubMedGoogle Scholar
  3. 3.
    Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA (1999) Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 24:153–159CrossRefPubMedGoogle Scholar
  4. 4.
    Hamadeh HK, Amin RP, Paules RS, Afshari CA (2002) An overview of toxicogenomics. Curr Issues Mol Biol 4:45–56PubMedGoogle Scholar
  5. 5.
    Tong W, Cao X, Harris S, Sun H, Fang H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, Shi L, Casciano D (2003) ArrayTrack—supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect 111:1819–1826CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Frueh FW (2006) Impact of microarray data quality on genomic data submissions to the FDA. Nat Biotechnol 24:1105–1107CrossRefPubMedGoogle Scholar
  7. 7.
    Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhong S, Zong Y, Slikker W Jr (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151–1161CrossRefGoogle Scholar
  8. 8.
    Guidance for Industry: Pharmacogenomic data submissions–Companion Guidance: Department of Health and Human Services (HHS), Food and Drug Administration (FDA) (August 2007) http://www.fda.gov/cder/guidance/7735dft.pdf
  9. 9.
    Clinical Data Interchange Standard Consortium (CDISC): CDISC Inc., 15907 Two Rivers Cove, Austin, Texas 78717 (2007) http://www.cdisc.org/index.html
  10. 10.
    Tong W, Harris S, Cao X, Fang H, Shi L, Sun H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, Casciano D (2004) Development of public toxicogenomics software for microarray data management and analysis. Mutat Res 549:241–253CrossRefPubMedGoogle Scholar
  11. 11.
    Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum Information About a Microarray Experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371CrossRefPubMedGoogle Scholar
  12. 12.
    Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32(Suppl):496–501CrossRefPubMedGoogle Scholar
  13. 13.
    Fielden MR, Halgren RG, Dere E, Zacharewski TR (2002) GP3: GenePix post-processing program for automated analysis of raw microarray data. Bioinformatics 18:771–773CrossRefPubMedGoogle Scholar
  14. 14.
    Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98:5116–5121CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Chen T, Guo L, Zhang L, Shi LM, Fang H, Sun YM, Fuscoe JC, Mei N (2006) Gene expression profiles distinguish the carcinogenic effects of aristolochic acid in target (kidney) and non-target (liver) tissues in rats. BMC Bioinformatics 7(Suppl 2):S20CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Sun H, Fang H, Chen T, Perkins R, Tong W (2006) GOFFA: Gene Ontology for Functional Analysis—a FDA Gene ontology tool for analysis of genomic and proteomic data. BMC Bioinformatics 7(Suppl 2):S23CrossRefPubMedCentralGoogle Scholar
  17. 17.
    Arlt VM, Ferluga D, Stiborova M, Pfohl-Leszkowicz A, Vukelic M, Ceovic S, Schmeiser HH, Cosyns JP (2002) Is aristolochic acid a risk factor for Balkan endemic nephropathy-associated urothelial cancer? Int J Cancer 101:500–502CrossRefPubMedGoogle Scholar
  18. 18.
    Shav-Tal Y, Zipori D (2002) The role of activin a in regulation of hemopoiesis. Stem Cells 20:493–500CrossRefPubMedGoogle Scholar
  19. 19.
    Fang H, Perkins R, Tong W (2007) Omics integrating systems using ArrayTrack and other bioinformatics tools. Am Drug Discov 2:49–52Google Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Hong Fang
    • 1
  • Stephen C. Harris
    • 2
  • Zhenjiang Su
    • 2
  • Minjun Chen
    • 2
  • Feng Qian
    • 1
  • Leming Shi
    • 2
  • Roger Perkins
    • 1
  • Weida Tong
    • 2
    Email author
  1. 1.Z-Tech Corporation, An ICF International CompanyJeffersonUSA
  2. 2.Division of Systems ToxicologyNational Center for Toxicological Research (NCTR), FDAJeffersonUSA

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