+This track is part of the DANIO-CODE track collection. CAGE (cap analysis of gene expression) sequences only the very first bases of capped RNA molecules. Each read therefore marks one transcription start site, at base resolution. Because promoters usually fire from a small cluster of neighboring start sites rather than a single base, the individual start sites are grouped into tag clusters, and a tag cluster is a good working definition of an active promoter.
This track shows CAGE data for 16 zebrafish samples spanning 12 developmental stages, from the 1-cell stage to the adult. Two kinds of data are shown: the raw signal, which is the number of transcription start sites seen at each base, and the tag clusters called from that signal. Zebrafish is a useful system for this because the promoters used by the mother's stored RNA and those used after the embryo's own genome switches on can sit within the same promoter region and are separable at this resolution.
--This track is part of the DANIO-CODE collection. -
-The track has two views that can be configured separately. Signal shows one coverage graph per sample, auto-scaled to the window. Regions shows the tag clusters as blocks; the score of a cluster reflects its expression, and the colors are taken from the consortium's files.
Nothing is displayed until samples are selected on the configuration page, where they can be filtered by developmental stage and by sample.