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ArrayTrack™ History

Install ArrayTrack

...a microarray database, data analysis, and data interpretation tool

 

The following criteria were considered at ArrayTrack’s inception and continue to be considered during continuing development: 

  1. A rich collection of gene, protein, and pathway functional information to provide context in data interpretation 
  2. A software environment that automatically integrates gene expression data with functional information and visual and analytic tools for efficient and effective data analysis and interpretation 
  3. Ability to cross-link gene expression and conventional toxicological data for phenotypic-driven exploration of underlying mechanisms of toxicity 
  4. Modularization for easy extensibility to other types of omics data (e.g., proteomic and metabonomic data) to enable systems toxicology research

ArrayTrack™, in its eight years of development, has witnessed tremendous growth and has established itself as a comprehensive data management, analysis, and interpretation tool. During this time it has had increasing and demonstrable impacts on FDA programs such as the Voluntary Genomics Data Submission (VGDS) program and the MicroArray Quality Control (MAQC) project.

ArrayTrack™ is widely used within FDA in important programs, and is also freely available to the entire scientific community. Its popularity has steadily grown, and its use has spread within public agencies (e.g., EPA, CDC, and NIH), academia, and private sector on an international scale. ArrayTrack™ has Web users (i.e., on the FDA Web site) as well as local installations where ArrayTrack™ is installed along with a local Oracle database. 

2001: Version 1.0.0

ArrayTrack™ was first developed as a research tool to support in-house microarray experiments using simple and inexpensive filter arrays.

2002-2003: Version 2.0.0

With the establishment of an in-house microarray core facility at NCTR, ArrayTrack™ was further developed to fulfill the requirement of a microarray data management, analysis, and interpretation tool. It was expanded to work with custom two color arrays. ArrayTrack™ was made available to the public in late 2003[1].

2004: Version 3.1.0

In 2004, ArrayTrack™ was adapted as the primary tool for FDA’s voluntary genomics data submission program (VGDS). The VGDS program is a novel data-submission mechanism which encourages regulated sponsors to interact with the FDA by submitting genomic data on a voluntary basis. ArrayTrack's adoption as the FDA genomic tool to support VGDS created additional functionality requirements, which led to an expansion of the software to work with Affymetrix GeneChip technology. New functionalities that were developed included:

    • direct loading of CEL files into ArrayTrack™
    • conversion of probe level data to any or all of the probe-set level data types including MAS5, RMA, DChip and Plier
    • data filtering based on the presence/absence call
    • mapping the affy ID to other types of gene IDs (e.g., Entrez Gene ID), protein ID (e.g., SwissProt Accession number), and different array platform ID (e.g., Agilent ID)
    • providing annotations (e.g., pathways, functions) 
2005-2006: Version 3.1.5-3.2.0

Through its use in the VGDS program, many key issues needed to be addressed such as array quality, data analysis methods, and cross-platform differences. In order to provide a consensus solution regarding the quality of microarray experiments, an NCTR-led collaborative effort, the MAQC project was started in 2005. The MAQC Phase I project used six different commercial and one institutionally developed microarray platform, requiring ArrayTrack™ to significantly expand in the type of arrays it supported. As a result, a generalized data management scheme was implemented that can handle data from most, if not all, commercial array platforms including Affymetrix, Agilent one and two color arrays, ABI, CodeLink and Illumina. ArrayTrack™ also integrated other external software such as Ingenuity, GeneLogic DrugMatrix, GeneGo MetaCore, CEBS, and SAS/JMP, thereby significantly building its data analysis and biological interpretation capabilities.

2007: Version 3.3.0

By the end of 2006 the VGDS program had been extended to proteomics and metabonomics data voluntary submissions and as a result, VGDS was renamed as VXDS (Voluntary eXploratory Data Submission). With VXDS submissions bringing forth a large amount of both clinical and non-clinical data, a requirement arose for a general mechanism to handle study data [2]. Such a general data standard was implemented in ArrayTrack™ using the Study Data Tabulation Model (SDTM) as the standard for non-clinical data and clinical data as suggested by Clinical Data Interchange Standard Consortium (CDISC). Additionally, functionalities were developed to facilitate interpretation of multiple data types (nonclinical, clinical and data from different omics platforms) in the context phenotypic anchoring.

2008-Present: Version 3.4.0

With the latest software version release, ArrayTrack™ has been expanded to include a new format for importing data called SimpleTox. The SimpleTox format utilizes controlled vocabulary from MIAME and SEND (Standard for Exchange of Nonclinical Data) to permit study data (e.g., animal data and toxicological endpoints) to be input along with corresponding array data. This allows for linking of expression data with phenotypic endpoints and enables identification of possible molecular mechanisms related to phenotype. Additional data analysis functions such as the popular SAM-Test, K-mean clustering have also been incorporated into the latest version. Also, a functionality to identify common pathways and/or GO terms shared by up to three lists of analytes has been implemented. The analytes may be from the same experimental platform, but different technologies such as genomics, proteomics, and metabolomics, thus expanding ArrayTrack's utility for system biology.

  1. Tong, W., et al. ArrayTrack™—supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environmental Health Perspectives. 2003. 111(15):1819-1826.
  2. Tong, W., et al. An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative. Drug Discovery Today. 2007. 4(1):3-8.

ArrayTrack™ is a product designed and produced by the National Center for Toxicological Research (NCTR). FDA and NCTR retain ownership of this product. 
© Copyright 2004-2013, NCTR/FDA.


 

 

Contact FDA

870-543-7000
National Center for Toxicological Research

Food and Drug Administration

3900 NCTR Road

Jefferson, AR 72079