ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research.

Abstract

The mapping of the human genome and the determination of corresponding gene functions, pathways, and biological mechanisms are driving the emergence of the new research fields of toxicogenomics and systems toxicology. Many technological advances such as microarrays are enabling this paradigm shift that indicates an unprecedented advancement in the methods of understanding the expression of toxicity at the molecular level. At the National Center for Toxicological Research (NCTR) of the U.S. Food and Drug Administration, core facilities for genomic, proteomic, and metabonomic technologies have been established that use standardized experimental procedures to support centerwide toxicogenomic research. Collectively, these facilities are continuously producing an unprecedented volume of data. NCTR plans to develop a toxicoinformatics integrated system (TIS) for the purpose of fully integrating genomic, proteomic, and metabonomic data with the data in public repositories as well as conventional (Italic)in vitro(/Italic) and (Italic)in vivo(/Italic) toxicology data. The TIS will enable data curation in accordance with standard ontology and provide or interface a rich collection of tools for data analysis and knowledge mining. In this article the design, practical issues, and functions of the TIS are discussed through presenting its prototype version, ArrayTrack, for the management and analysis of DNA microarray data. ArrayTrack is logically constructed of three linked components: a) a library (LIB) that mirrors critical data in public databases; b) a database (MicroarrayDB) that stores microarray experiment information that is Minimal Information About a Microarray Experiment (MIAME) compliant; and c) tools (TOOL) that operate on experimental and public data for knowledge discovery. Using ArrayTrack, we can select an analysis method from the TOOL and apply the method to selected microarray data stored in the MicroarrayDB; the analysis results can be linked directly to gene information in the LIB.

The Liver Toxicity Biomarker Study: Phase I Design and Preliminary Results

“…With regard to the overall biological interpretation of the results of phase I, a variety of data integration and data mining approaches are being used at the NCTR and at BG Medicine, including ArrayTrack (Tong et al 2003;Tong et al 2004), Ingenuity Pathways Analysis (Ingenuity Systems, Redwood City, CA, USA), and Correlation Network Analysis (Adourian et al 2008). One focus of this analysis is to determine whether there is evidence of mitochondrial uncoupling in the integrated molecular profiling dataset for the effects of tolcapone on rat liver, as has been suggested by the previous comparisons of the actions of entacapone and tolcapone (Haasio et al 2001;Haasio et al 2002).…”

Self-self Hybridization As An Alternative Experiment Design to Dye Swap for Two-color Microarrays

“…Data analyses were conducted using FDA microarray software ArrayTrack (Tong et al, 2003;Tong et al, 2004). ArrayTrack is generally available through the FDA website (Ͻhttp://edkb.fda.gov/webstart/ arraytrackϾ).…”

Development of public toxicogenomics software for microarray data management and analysis

“…2A), ProteinLib and PathwayLib. As the names suggest, these three libraries concentrate functional information on genes, proteins and pathways, respectively [5]. The user can quickly identify the functional information for a set of significant genes derived from analysis by searching these libraries.…”

“…Correspondingly, a microarray data management, analysis and interpretation software system, ArrayTrack, has been developed to address the bioinformatics challenges associated with microarray experiment [5].…”