Radiation Genes: a database devoted to microarrays screenings revealing transcriptome alterations induced by ionizing radiation in mammalian cells

Abstract

The analysis of the great extent of data generated by using DNA microarrays technologies has shown that the transcriptional response to radiation can be considerably different depending on the quality, the dose range and dose rate of radiation, as well as the timing selected for the analysis. At present, it is very difficult to integrate data obtained under several experimental conditions in different biological systems to reach overall conclusions or build regulatory models which may be tested and validated. In fact, most available data is buried in different websites, public or private, in general or local repositories or in files included in published papers; it is often in various formats, which makes a wide comparison even more difficult. The Radiation Genes Database (http://www.caspur.it/RadiationGenes) collects microarrays data from various local and public repositories or from published papers and supplementary materials. The database classifies it in terms of significant variables, such as radiation quality, dose, dose rate and sampling timing, as to provide user-friendly tools to facilitate data integration and comparison.

Figure 1.

The software architecture of the system.

Figure 2.

Screenshot of the submission form prepared according to a simplified and modified MIAME protocol. Notice that dose, dose rate and quality of radiation have been added to the experimental factors to be specified.

Figure 3.

Hierarchical clustering of data for 18 genes which pass the log₂ ratio cut-off: >1 in at least 20% of the experiments. Gene tree and conditions tree clustering were performed by selecting the following parameters: Euclidean distance and complete linkage. The condition tree has been zoomed by using the online tools and horizontally separated in three areas: the left portion (A) the central part (B) and the right portion (C).