Compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS contains over 11000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data. The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets.
Provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types.
A toxicogenomics database that stores gene expression profiles and traditional toxicological data derived from in vivo (rat) and in vitro (primary rat hepatocytes, primary human hepatocytes) exposure to 170 compounds at multiple dosages and time points.
Covers toxicogenomic signatures. TOXsIgN aims to archive heterogeneous data and allows users to upload lists of overexpressed/underexpressed genes from different omics experiments. It can provide data usable for cross-species and cross-technology comparisons. This database contains over 750 projects for about 900 transcriptomic studies of more than 450 compounds performed in humans, rats, mice, or drosophila.
A robust and sustainable infrastructure storing toxicogenomics data. A central data warehouse is connected to a portal with links to chemical information and molecular and phenotype data. diXa is publicly available through a user-friendly web interface. New data can be readily deposited into diXa using guidelines and templates available online. Analysis descriptions and tools for interrogating the data are available via the diXa portal.
An online web server for easy and fast visualization of smoking effects on human lung gene expression. SEGEL integrates 362 samples collected from eight public expression microarray data sets from trachea epithelial cells, large airway epithelial cells, small airway epithelial cells, and alveolar macrophage. Gene expression patterns of regular smokers and nonsmokers across these cells can be queried by gene symbols. Sex difference in response to smoking is also shown. The correlation coefficients between the gene expression and cigarette smoking consumption (the number of packs of cigarettes consumed per year) were also calculated and are shown in the web server. The current version of SEGEL contains around 42,400 annotated gene probe sets represented on the Affymetrix Human Genome U133 Plus 2.0. SEGEL will be an invaluable tool and resource for scientists interested in the effects of smoking on lung gene expression. The web server can be used to identify reliable molecular signatures for drug discovery against smoking-related diseases.
A resource that analyzes drug-induced gene expression changes at the pathway level. We have collected 2694 pathway concepts and computed numerical response scores of these pathways for 437 drugs and chemicals and 7464 different experimental conditions. ToxDB provides functionalities for exploring these pathway responses by offering tools for visualization and differential analysis allowing for comparisons of different treatment parameters and for linking this data with toxicity annotation and chemical information. ToxDB builds on three components: (i) a comprehensive collection of pathway concepts along with drug treatment microarray data, (ii) a numerical method to compute pathway responses from genome-scale expression data, (iii) a web interface that enables user interaction.