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FDA Genomic Tool: ArrayTrack™
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A free bioinformatics resource for DNA microarray and systems biology
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Allows for the management, analysis and interpretation of omics data
within a single package
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Utilized by the U.S. FDA for the review of
genomic data submissions. [WORD]
ArrayTrack™ provides an integrated solution for managing,
analyzing, and interpreting microarray gene expression data.
Specifically, ArrayTrack™ is MIAME (Minimum Information About A
Microarray Experiment) supportive for storing both microarray data and
experiment parameters associated with a pharmaco- or toxico- genomics
study. Many statistical and visualization tools are available with ArrayTrack™. ArrayTrack™ also provides a rich collection of functional
information about genes, proteins and pathways for biological
interpretation. The primary emphasis of ArrayTrack™ is the direct linking
of analysis results with functional information for facilitating the
interaction between the choice of analysis methods and the biological
relevance of analysis results. Using ArrayTrack™, user can easily select
a statistical method applied to a stored microarray data to determine a
list of differentially expressed genes and the gene list can be directly
linked to pathways and gene ontology for functional analysis.
ArrayTrack™ News
WHAT’s NEW:
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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, 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)
- NEW RELEASE: ArrayTrack™ v3.4.0
Release Announcement
(1/31/2008 Web version)(6/30/2008 CD version).
- A new batch data uploading
format, called SimpleTox, is available. SimpleTox was developed
based on the SEND
v2.3(Standard
for Exchange of Nonclinical Data)
standard and the SDTM (Study Data
Tabulation Model) data model, and as such supports most non-clinical
studies in conjunction with DNA microarrays. Data uploaded using
SimpleTox is searchable (12/31/2007).
Check it out!
- The R version of the very
popular SAM (Significance Analysis
of Microarrays, SAMR v1.25) has been integrated with ArrayTrack™. You can access
and run SAM within ArrayTrack™ with a user friendly interface
(12/31/2007). Enjoy!
- In addition to Windows and
UNIX, ArrayTrack™ now supports Linux SuSE 10, Linux RedHat Enterprise
3, Linux Ubuntu 7 (10/31/2007).
WHAT's COMING: Integrating ArrayTrack™ with
the JANUS database has begun. This
effort will result in a complete data repository solution aggregating
and integrating clinical and non-clinical study data together with DNA
microarray data (08/29/2007)
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ArrayTrack™ tutorials are available (6/20/06).
- ArrayTrack™ DrugMatrix initial integration is complete.
(6/20/06).
- ArrayTrack™-GeneGo MedaCore integration is complete (02/06).
- ArrayTrack™-JMP Genomics integration accomplished (12/05).
The JMP Genomics software (developed by SAS) is an extension of the
classic JMP for analysis of microarray and other omics data.
This integration allows data to be exported/imported between
ArrayTrack™ and JMP Genomics.
- ArrayTrack™-IPA integration: ArrayTrack™ is integrated with
Ingenuity Pathways Analysis (IPA) developed by Ingenuity Systems. The
integration allows results in ArrayTrack™ (e.g., a list of genes from a microarray experiment) directly link to IPA for analysis. (06/05)
- ArrayTrack™-CEBS integration: The National Center for
Toxicological Research (NCTR/FDA) and National Institute of
Environmental Health Sciences (NIEHS) entered an interagency agreement
(IAG) to make ArrayTrack™ and Chemical Effects in Biological Systems (CEBS)
developed by NIEHS fully interoperable. The latest versions of the two
products will be made publicly available late in calendar year 2005.
(05/05)
- ArrayTrack™-SAS SDS integration: The National Center for
Toxicological Research (NCTR/FDA) establishes Cooperative Research and
Development Agreement (CRADA) with SAS Institute Inc. to develop
ArrayTrack™ modules to linking functionality of ArrayTrack™ with SAS
Scientific Discovery Solution (SDS). (04/05)
- ArrayTrack™-PathArt integration: ArrayTrack™ is integrated
with PathArt (Jubilant Biosys). Through ArrayTrack™, user can access
various pathways provided in PathArt. (08/04)
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Download:
Quick Help Manual in 508 compliant
PDF
format. Access ArrayTrack™
Tutorials
Help Manual will be available in the near future.
Sample Data |
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For any collaboration, please contact Dr. Weida Tong at +1-870-543-7142 (voice) or
weida.tong@fda.hhs.gov.
Please address any questions and suggestions
to Dr. Hong Fang at +1-870-543-7538 (voice) or
hong.fang@fda.hhs.gov
For any technical problems and
bugs, please e-mail to
NCTR
Bioinformatics Support .
For more information, please visit the
NCTR/FDA's
Center for Toxicoinformatics.
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