ABSTRACT
Cap Analysis of Gene Expression (CAGE) produces a large number of 5'-end short reads of transcripts, which represent two aspects of transcrip tome: transcriptional starting site as a part of gene structure and transcriptional initiation activity in a certain biological samples. This chapter discusses databases and visualization tools to handle CAGE data. It reviews public databases to store such data, and introduce methods enabling to use CAGE data. CAGE allows analyzing at least two aspects of transcription events in transcriptome level: the genomic locations of transcriptional initiation and the activity of all the core promoters driving specific transcription. Published CAGE tags are available in public databases, where the stored content is different depending on the database. The genome view enables us to inspect transcriptional initiation events in association with other elements encoded in the genome, and such view is adopted in many databases.
