148
D. L. Svoboda et al.
Table 8.1 DrugMatrix GUI data domains
Data domains
Contents
Gene
Presents all relevant information from the database for a queried gene,
such as annotation, genes that exhibit similar expression patterns,
treatments that induce or repress the gene, molecular pharmacology results
and activities reported in the literature
Compound
Presents all relevant information from the database for a queried
compound, such as chemicals with similar structures, genes that are
induced or repressed by the compound, experiments where the chemical
was used, molecular pharmacology results for the compound and literature
annotations
Assay
Presents all relevant information from the database for a queried molecular
pharmacology, clinical chemistry or hematology assay, such as which
chemicals were active and details on the assay and its associated gene(s)
Expression
Presents all relevant information from the database for a queried
experiment (a single chemical, time point, dose, tissue, species, and array
type) such as experiments with similar expression patterns, genes that were
induced or repressed in an experiment, and the clinical chemistry,
hematology and histopathology results for the experiment
Pathway
Provides information on the hand-curated biochemical, metabolic and
signal transduction pathways annotated in DrugMatrix
Expression Study
Presents a list of experiments related to the queried study. A study is a
collection of data representing a multi-dose and time point toxicity
assessment. Information about a study such as time course, dose
justification, pathlab report, and dose justification is found in this domain
Motif
Presents all relevant information from the database for a queried signature
motif. A Motif is a pathway-centric gene expression signature that
classifies a toxicity endpoint. Information about a motif such as similarity
to other motifs, genes contained in the motif, and experiments that is active
Signature
Presents all relevant information from the database for a queried
DrugMatrix signature. Signatures are similar to motifs with the exception
that the signatures are not limited to pathway genes. Information contained
in this domain parallels that for the Motif domain
blood chemistry, and histopathology data is described. The algorithms and computations that form the basis of the drug signatures are elaborated in detail, as well as
the analytical tools that are utilized to assist data visualization and interpretation in
the DrugMatrix GUI. In addition, compound curation, pathway curation, and gene
annotation processes are described in this document.
8.4 DrugMatrix GUI
The DrugMatrix GUI (Fig. 8.4) consists of: (1) A set of sophisticated querying
tools that enables queries that filter by expression profile, chemical structure, gene
names, compound names, or by the presence of any attribute (e.g., a compound that
D. L. Svoboda et al.
Table 8.1 DrugMatrix GUI data domains
Data domains
Contents
Gene
Presents all relevant information from the database for a queried gene,
such as annotation, genes that exhibit similar expression patterns,
treatments that induce or repress the gene, molecular pharmacology results
and activities reported in the literature
Compound
Presents all relevant information from the database for a queried
compound, such as chemicals with similar structures, genes that are
induced or repressed by the compound, experiments where the chemical
was used, molecular pharmacology results for the compound and literature
annotations
Assay
Presents all relevant information from the database for a queried molecular
pharmacology, clinical chemistry or hematology assay, such as which
chemicals were active and details on the assay and its associated gene(s)
Expression
Presents all relevant information from the database for a queried
experiment (a single chemical, time point, dose, tissue, species, and array
type) such as experiments with similar expression patterns, genes that were
induced or repressed in an experiment, and the clinical chemistry,
hematology and histopathology results for the experiment
Pathway
Provides information on the hand-curated biochemical, metabolic and
signal transduction pathways annotated in DrugMatrix
Expression Study
Presents a list of experiments related to the queried study. A study is a
collection of data representing a multi-dose and time point toxicity
assessment. Information about a study such as time course, dose
justification, pathlab report, and dose justification is found in this domain
Motif
Presents all relevant information from the database for a queried signature
motif. A Motif is a pathway-centric gene expression signature that
classifies a toxicity endpoint. Information about a motif such as similarity
to other motifs, genes contained in the motif, and experiments that is active
Signature
Presents all relevant information from the database for a queried
DrugMatrix signature. Signatures are similar to motifs with the exception
that the signatures are not limited to pathway genes. Information contained
in this domain parallels that for the Motif domain
blood chemistry, and histopathology data is described. The algorithms and computations that form the basis of the drug signatures are elaborated in detail, as well as
the analytical tools that are utilized to assist data visualization and interpretation in
the DrugMatrix GUI. In addition, compound curation, pathway curation, and gene
annotation processes are described in this document.
8.4 DrugMatrix GUI
The DrugMatrix GUI (Fig. 8.4) consists of: (1) A set of sophisticated querying
tools that enables queries that filter by expression profile, chemical structure, gene
names, compound names, or by the presence of any attribute (e.g., a compound that