8 An Overview of National Toxicology Program’s Toxicogenomic …
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audience, it remains a valuable resource for toxicologists and researchers. It continues to be a, perhaps unsurpassed, example of the power of data integration for
genomic toxicology.
DrugMatrix is an exceptional tool for data exploration, and it provides a vast
landscape of information that can be challenging to formulate into a single report.
Feedback from end users in relation to this issue led Iconix to create ToxFX. By
combining the highly curated data in DrugMatrix with templated text processing,
ToxFX carries out rapid and automated interpretation and reporting of toxicogenomic
study results. In less than 5 min, ToxFX transforms normalized differential gene
expression data files, along with simple user-provided data annotations to a detailed
report covering numerous levels of interpretation along with supporting data tables,
histopathology section images, and other visualizations.
The National Toxicology Program (NTP) took ownership of DrugMatrix and
ToxFX and all associated assets in 2010 after it was briefly owned by Entelos. The
goal of the acquisition was to make the resources freely available to the research
community. Since this time the data, in particular the transcriptomics data, has been
extensively reused and broadly circulated. As of this writing, NTP has made the
entire contents of the DrugMatrix Database available in multiple forms and has
made DrugMatrix and ToxFX available via an open-source distribution to enable
users to deploy their own installation of the software.
Throughout this book chapter, different components of DrugMatrix will be
referred to. When referring to the DrugMatrix database, we are indicating the
relational database (PostgreSql) that holds all the DrugMatrix data that may be
downloaded elsewhere (ftp://anonftp.niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/
DrugMatrixPostgreSqlDatabase.tar.gz). The DrugMatrix-browser-based GUI that
allows end users to query the database via a server-based application, will be called
the DrugMatrix GUI. These two taken together, along with other associated assets
will be referred to as DrugMatrix.
8.2 DrugMatrix Data
The DrugMatrix Database is a highly integrated rat toxicogenomics database containing one of the largest, systematically created collections of data of interest to
toxicologists. It is built using the results of short-term toxicogenomic studies on
>600 reference drugs/chemicals (433 US Food and Drug Administration (FDA)
approved drugs, 63 drugs approved outside the USA, 54 withdrawn or discontinued
drugs, 15 standard biochemicals, and 72 standard toxicants) in male Sprague Dawley
rats. It is composed of the results of over 5000 Affymetrix 230 2.0 and 12,000 GE
Codelink microarray studies performed on samples from liver, kidney, heart, thigh
muscle, bone marrow, spleen, brain, intestine, and primary hepatocytes. In addition,
127,000 histopathology, and ~100,000 hematology and clinical chemistry measurements were taken to enable cross-referencing gene expression results in established
toxicity metrics. In addition to the data from the animal studies, the database also
143
audience, it remains a valuable resource for toxicologists and researchers. It continues to be a, perhaps unsurpassed, example of the power of data integration for
genomic toxicology.
DrugMatrix is an exceptional tool for data exploration, and it provides a vast
landscape of information that can be challenging to formulate into a single report.
Feedback from end users in relation to this issue led Iconix to create ToxFX. By
combining the highly curated data in DrugMatrix with templated text processing,
ToxFX carries out rapid and automated interpretation and reporting of toxicogenomic
study results. In less than 5 min, ToxFX transforms normalized differential gene
expression data files, along with simple user-provided data annotations to a detailed
report covering numerous levels of interpretation along with supporting data tables,
histopathology section images, and other visualizations.
The National Toxicology Program (NTP) took ownership of DrugMatrix and
ToxFX and all associated assets in 2010 after it was briefly owned by Entelos. The
goal of the acquisition was to make the resources freely available to the research
community. Since this time the data, in particular the transcriptomics data, has been
extensively reused and broadly circulated. As of this writing, NTP has made the
entire contents of the DrugMatrix Database available in multiple forms and has
made DrugMatrix and ToxFX available via an open-source distribution to enable
users to deploy their own installation of the software.
Throughout this book chapter, different components of DrugMatrix will be
referred to. When referring to the DrugMatrix database, we are indicating the
relational database (PostgreSql) that holds all the DrugMatrix data that may be
downloaded elsewhere (ftp://anonftp.niehs.nih.gov/ntp-cebs/datatype/Drug_Matrix/
DrugMatrixPostgreSqlDatabase.tar.gz). The DrugMatrix-browser-based GUI that
allows end users to query the database via a server-based application, will be called
the DrugMatrix GUI. These two taken together, along with other associated assets
will be referred to as DrugMatrix.
8.2 DrugMatrix Data
The DrugMatrix Database is a highly integrated rat toxicogenomics database containing one of the largest, systematically created collections of data of interest to
toxicologists. It is built using the results of short-term toxicogenomic studies on
>600 reference drugs/chemicals (433 US Food and Drug Administration (FDA)
approved drugs, 63 drugs approved outside the USA, 54 withdrawn or discontinued
drugs, 15 standard biochemicals, and 72 standard toxicants) in male Sprague Dawley
rats. It is composed of the results of over 5000 Affymetrix 230 2.0 and 12,000 GE
Codelink microarray studies performed on samples from liver, kidney, heart, thigh
muscle, bone marrow, spleen, brain, intestine, and primary hepatocytes. In addition,
127,000 histopathology, and ~100,000 hematology and clinical chemistry measurements were taken to enable cross-referencing gene expression results in established
toxicity metrics. In addition to the data from the animal studies, the database also