The toxicogenomics studies in the diXa warehouse are complemented by publically available disease datasets. The 188 disease datasets fall into three sub-categories: liver, kidney and cardiovascular disease.
The majority of the available disease data are mRNA expression profiles, but some other data types are available (e.g. miRNA expression data, single nucleotide polymorphisms/genome wide association studies, mutation studies, copy number variation studies, and DNA methylation data).
Searching for disease data
The diXa warehouse includes ICD-10 terms for the human disease datasets. You can search the disease data by organ, by using a disease-related term or by entering the numeric or the textual part of an ICD-10 term.
Figure 9 Disease details page.
The disease details page (Figure 9) provides you with the source of the data, a short study description and the ICD-10 terms (which can be used to start a new search query). If applicable, the links to the original datasets in ArrayExpress are provided, together with the re-annotated metadata files that include ICD-10 terms and codes.
The Comparative Toxicogenomics Database (CTD) provides information on whether a specific compound is likely to cause/interfere with a particular disease. The compounds represented in the diXa warehouse were screened for a relation to the liver, kidney and/or cardiovascular system using the CTD database. If an association was present for one these ‘organs’, you will find a link to the human disease data for that particular organ on the compound details page (Figure 11).