TransgenicDB is a relational database that incorporates data from studies published to date and unpublished data contributed by several members of the International Workshops on Genotoxicity Testing (IWGT) working group. We have used the TrannsgenicDB to analyse trends in the data and to extract information regarding several key parameters of test performance.
The core is an experimental data table that contains details of 3186 experimental records identified in the literature as well as several complete but not yet published experimental records that have been contributed by members of the IWGT working group. The experimental records contained in the TransgenicDB consist of comparisons between a treatment and a control group; data are not included if the study is limited to an examination of spontaneous mutation or DNA sequence analysis.
Information for the genotoxicity and carcinogenicity data table was derived from the Gene-Tox and Chemical Carcinogenesis Research Information System databases (http://toxnet.nlm.nih.gov), the Genetic Activity Profiles database (Waters et al., 1991) and the published scientific literature.
The Mutation assay Spectral Database (MGMD) is a comprehensive collection of published mutation data from the open literature on mammalian cell-based gene model mutation detection systems. The database currently contains approximately 30000 comprehensively described mutant spectra records and it is maintained and up- dated on a daily basis.
The major objectives of the MGMD were (i) to provide an Internet-accessible database for chemically induced and spontaneous mutation types and spectra in selected genes; (ii) to standardize the reporting of mutations within different genes where ambiguity exists in the literature; and (iii) to provide interactive and user-friendly access to the information.
A multi-option search facility has been included that allows the user to search the database for parameters such as mutagen, gene or cell type of interest. The structure of the database permits easy retrieval of specific mutation data for further analysis. Thus, the MGMD should become a useful and necessary reference source and provides an analysis tool for genetic toxicologists.
Drsmooth provides tools for assessing the shape of a dose-response curve by testing linearity and non-linearity
at user-defined cut-offs.
It also provides two methods of estimating a threshold dose, or the dose at which the dose-response function
transitions to significantly
increasing: bi-linear (based on pkg:segmented) and smoothed with splines (based on pkg:mgcv).
(from http://cran.r-project.org/web/packages/drsmooth/index.html )
The sensitivity of any mutational assay is determined by the level at which spontaneous mutations occur in the corresponding untreated controls. Establishing the type and frequency at which mutations occur naturally within a test system is essential if one is to draw scientifically sound conclusions regarding chemically induced mutations. iMARS is a comprehensive mutation-spectrum analysis package that utilises routinely used methodologies and visualisation tools.
Institute of Life Science, College of Medicine, Swansea University, UK