Cap-analysis gene expression (CAGE) Basic and Analysis Databases store an original resource produced by CAGE, which measures expression levels of transcription starting sites by sequencing large amounts of transcript 5' ends, termed CAGE tags. Millions of human and mouse high-quality CAGE tags derived from different conditions in >20 tissues consisting of >250 RNA samples are essential for identification of novel promoters and promoter characterization in the aspect of expression profile. CAGE Basic Database is a primary database of the CAGE resource, RNA samples, CAGE libraries, CAGE clone and tag sequences and so on. CAGE Analysis Database stores promoter related information, such as counts of related transcripts, CpG islands and conserved genome region. It also provides expression profiles at base pair and promoter levels. Both databases are based on the same framework, CAGE tag starting sites, tag clusters for defining promoters and transcriptional units (TUs). Their associations and TU attributes are available to find promoters of interest. These databases were provided for Functional Annotation Of Mouse 3 (FANTOM3), an international collaboration research project focusing on expanding the transcriptome and subsequent analyses. Now access is free for all users through the World Wide Web at http://fantom3.gsc.riken.jp/.