150
D. L. Svoboda et al.
Domain Report contains a subset of Chemogenomic Data Reports and Detail Reports
that present cross-referenced experimental data from the DrugMatrix database, and
curated information from the scientific literature, reference material, and online
databases. As operations are executed within the DrugMatrix framework (for example, conduct queries, save lists, or access previously saved lists) Server Status Messages appear at the bottom right of the User Interface, indicating progress of retrieval
of the requested operation.
The Search and List area of the DrugMatrix GUI consists of tools for generating
Simple Searches and Advanced Searches of the database, as well as a user-owned
Workspace with tools for the management of lists generated by these searches. Lists
that have been generated by database searches, previously saved user lists that have
been retrieved, Data Objects, and Favorite items are all available for use in the
Workspace area.
In addition to the data content that can be accessed through the DrugMatrix GUI,
several analysis tools are contained within the toolbox component of the interface
which enables analysis of uploaded data or data contained in the database (Table 8.2).
The TOOLBOX button, located on the WORKSPACE panel, opens a window containing these tools. A list of these tools can be found in Table 8.2. The analysis tools
are further described in the reference manual and in the materials and methods of
white papers in the help section of DrugMatrix.
A user can perform a wide-ranging number of tasks using the DrugMatrix GUI
such as: Upload your own data for analysis or mine the DrugMatrix data; find
similar expression profiles; determine significantly up- and down-regulated genes;
visualize expression profiles on pathways; construct expression patterns for putative biomarker sets; perform gene ontology analysis of perturbed genes; score gene
expression signatures; test performance of a biomarker set for detecting phenotypes;
perform hierarchical clustering; find consistently changed genes; identify enriched
literature annotations in groups of expression profiles and mine the literature. A
detailed tutorial with multiple detailed examples on how to use the DrugMatrix
GUI can be found elsewhere (ftp://anonftp.niehs.nih.gov/ntp-cebs/datatype/Drug_
Matrix/DrugMatrix_Tutorial.pdf).
8.5 ToxFX
ToxFX is an automated toxicogenomics analysis and reporting tool. It employs DrugMatrix gene expression data, pathway information, and toxicity signatures to formulate detailed reports, and supplementary results files from user-provided gene expression data sets. Each report contains an executive summary, study description, details
of the quality control metrics, relative impact on transcription, DM signature scores,
relative response of pathways, cytochrome P450 changes, and most consistent gene
expression changes. Less than 5 min is typically required from upload of normalized
data to output of a report.
D. L. Svoboda et al.
Domain Report contains a subset of Chemogenomic Data Reports and Detail Reports
that present cross-referenced experimental data from the DrugMatrix database, and
curated information from the scientific literature, reference material, and online
databases. As operations are executed within the DrugMatrix framework (for example, conduct queries, save lists, or access previously saved lists) Server Status Messages appear at the bottom right of the User Interface, indicating progress of retrieval
of the requested operation.
The Search and List area of the DrugMatrix GUI consists of tools for generating
Simple Searches and Advanced Searches of the database, as well as a user-owned
Workspace with tools for the management of lists generated by these searches. Lists
that have been generated by database searches, previously saved user lists that have
been retrieved, Data Objects, and Favorite items are all available for use in the
Workspace area.
In addition to the data content that can be accessed through the DrugMatrix GUI,
several analysis tools are contained within the toolbox component of the interface
which enables analysis of uploaded data or data contained in the database (Table 8.2).
The TOOLBOX button, located on the WORKSPACE panel, opens a window containing these tools. A list of these tools can be found in Table 8.2. The analysis tools
are further described in the reference manual and in the materials and methods of
white papers in the help section of DrugMatrix.
A user can perform a wide-ranging number of tasks using the DrugMatrix GUI
such as: Upload your own data for analysis or mine the DrugMatrix data; find
similar expression profiles; determine significantly up- and down-regulated genes;
visualize expression profiles on pathways; construct expression patterns for putative biomarker sets; perform gene ontology analysis of perturbed genes; score gene
expression signatures; test performance of a biomarker set for detecting phenotypes;
perform hierarchical clustering; find consistently changed genes; identify enriched
literature annotations in groups of expression profiles and mine the literature. A
detailed tutorial with multiple detailed examples on how to use the DrugMatrix
GUI can be found elsewhere (ftp://anonftp.niehs.nih.gov/ntp-cebs/datatype/Drug_
Matrix/DrugMatrix_Tutorial.pdf).
8.5 ToxFX
ToxFX is an automated toxicogenomics analysis and reporting tool. It employs DrugMatrix gene expression data, pathway information, and toxicity signatures to formulate detailed reports, and supplementary results files from user-provided gene expression data sets. Each report contains an executive summary, study description, details
of the quality control metrics, relative impact on transcription, DM signature scores,
relative response of pathways, cytochrome P450 changes, and most consistent gene
expression changes. Less than 5 min is typically required from upload of normalized
data to output of a report.