Install ArrayTrack™
...a microarray database, data analysis, and data interpretation tool
ArrayTrack™ Online Training Session
February 2, 2012
10:00 AM Central Time
Space is limited. Please e-mail don.ding@fda.hhs.gov to register.
10:00 AM Central Time
Space is limited. Please e-mail don.ding@fda.hhs.gov to register.
ArrayTrack™ News Update
- ArrayTrack™ News Update
- The ArrayTrack™ 3.5 Manual and User Guide for KNN and LDA have been published. The ArrayTrack™ 3.5 version of the Quick Start Manual and Tutorials have been updated as well.
- ArrayTrack™ web training is available once every two months.
- Standalone GOFFA Application Released
GOFFA is a tool developed for ArrayTrack™ that takes a list of genes and identifies terms in Gene Ontology (GO)associated with those genes. GOFFA provides:
- Tools to view both the GO term hierarchy and a full listing of GO terms annotated with the genes associated with each term
- Two statistical measurements available for significant of the GO term in a submitted gene list:
- Fisher's exact test p-value providing the probability of identifying the same number of genes for a given term by chance alone.
- Relative enrichment factor (E-value) giving the enrichment of a GO term for genes in the submitted list, relative to the frequency of genes assigned to that term from the full set of GOFFA annotated genes for a particular species
- Two novel methods to visualize and interpret results, GOPath and GO TreePrune. GO Path simultaneously displays the ranks that order GOFFA Tree Paths based on statistical analysis. GO TreePrune provides a visual display of a reduced GO term set based on a user's statistical cut-offs. A more complete description of GOFFA's abilities and functions has been published in BMC Bioinformatics
- SNPTrack Released
The ArrayTrack™ team has just released SNPTrack, an integrated suite for the management, analysis, and interpretation of genetic polymorphism data. SNPTrack stores and organizes study data and provides access to functional information about the SNPs (Single Nucleotide Polymorphism) in a study, including information about the genes and proteins containing a SNP, and Gene Ontology information and pathway information available for those genes and proteins. The client application integrates the popular analysis tools PLINK and Haploview with the storage and interpretation capabilities developed for ArrayTrack™. (11/03/10) - Locally Installed ArrayTrack™ 3.5.0 Available
The locally installed version of ArrayTrack™ 3.5.0 has been released. This option is well suited for larger groups with access to an Oracle database and a database administrator. To request a DVD of ArrayTrack™ 3.5.0, please send an e-mail to NCTRBioinformaticsSupport@fda.hhs.gov. (08/18/10) - ArrayTrack™ v3.5.0 Released
ArrayTrack™ 3.5.0 is now available for download. This update includes
- Model building capabilities using linear discriminant analysis (LDA) or k-nearest neighbors (KNN)
- Two all new libraries (SNP and QTL)
- The ability to analyze proteomics and metabolomics data
- Updates to GOFFA and existing ArryTrack™ libraries
- Simpler data import using a new Experiment Wizard
Learn more about these improvements. (03/03/10)
- SNP Library
An SNP Library has been added to the ArrayTrack™ Library collection. The SNP Library allows researchers to query SNP annotation for a list of SNPs. Furthermore, it provides SNP-related gene, protein, pathway, and Gene Ontology information. (03/16/2009) - SNP Data Analysis
An addition to the ArrayTrack™ suite that is specifically for SNP data analysis is underway. It is currently in the internal evaluation and testing phase. (03/09/09) - FDA "Commissioner’s Comments to FDA Staff" by Acting Commissioner, Frank M. Torti, MD, MPH
“NCTR has developed ArrayTrack™, a software tool that can store, analyze, and interpret DNA microarray data. Microarrays produce myriad data on gene expression that can provide added data on underlying mechanism of drug action for reviewers. To date, more than 100 FDA reviewers and scientists have been trained in the use of this software. This tool, in conjunction with the NCTR-led MicroArray Quality Control (MAQC) consortium and the Voluntary Genomics Data Submission (VGDS) process, is being used by several FDA regulatory centers to assess data voluntarily submitted by the regulated industry. This collaboration is one that identifies FDA as a catalyst in the development of new standards that will facilitate drug development.” (03/02/09) - ArrayTrack™ Successfully Implemented at Eli Lilly
On December 18, 2008, ArrayTrack™ 3.4 was set up and implemented at Eli Lilly as part of their production environment. The first trial of gene-expression data was also loaded into the stand-alone database successfully. Eli Lilly attributed the ArrayTrack™ team’s “high level of engagement, responsiveness and expertise” as the reason for “one of the best external engagements that I have experienced on an implementation project.” (02/09/09) - Eli Lilly Selects ArrayTrack™ArrayTrack™ is a free, publicly available bioinformatics tool developed by the NCTR for FDA research and review of pharmacogenomics data submitted by the sponsors in the Voluntary Genomics Data Submission (VGDS) program. ArrayTrack™ has been expanded to other omics dataset types, and over 100 FDA scientists and reviewers have been trained to use the ArrayTrack™ tools. Recently, Eli Lilly formed an evaluation team of experts for a rigorous review of ArrayTrack's architectural structure, functional, quality, and security assessments, local installation parameters, and ability to support Eli Lilly's clinical gene-expression studies. Eli Lilly selected the ArrayTrack™ platform for their clinical gene-expression data storage and baseline analysis and further stated, “The level of commitment demonstrated by the ArrayTrack™ group strengthened our confidence in our ability to work together on some of the current gaps in making ArrayTrack™ fully functional for Lilly scientists.” (7/31/2008)
- ArrayTrack™ v3.4.0 ReleasedRelease Announcement (1/31/2008-Web version and 6/30/2008-CD version)
- SimpleTox AvailableSimpleTox, a batch-data uploading format, was developed based on the SEND v2.3
- SAM Integrated with ArrayTrack™
The R version of the very popular SAM - ArrayTrack™ Supports Linux
Linux SuSE 10, Linux RedHat Enterprise 3, Linux Ubuntu 7, as well as Windows and UNIX, are supported by ArrayTrack™. (10/31/2007) - Integrating ArrayTrack™ and JANUS database
The integration of ArrayTrack™ and the JANUS database
Contact Information
Collaboration information: Dr. Weida Tong (870-543-7142 or weida.tong@fda.hhs.gov)
Assistance in using ArrayTrack™: Feng Qian (870-543-7290 or feng.qian@fda.hhs.gov)
Don Ding (870-543-7685 or don.ding@fda.hhs.gov)
Submit suggestions: Dr. Hong Fang (870-543-7538 or hong.fang@fda.hhs.gov)
Report technical problems: NCTRBioinformaticsSupport@fda.hhs.gov
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ArrayTrack™ is a product designed and produced by the National Center for Toxicological Research (NCTR). FDA and NCTR retain ownership of this product.
© Copyright 2004-2011, NCTR/FDA.
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Contact FDA
870-543-7000National Center for Toxicological Research
Food and Drug Administration
3900 NCTR Road
Jefferson, AR 72079
ArrayTrack<sup>TM</sup> > ArrayTrack™ News
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