Fig. 1

Data preparation and parameter settings. The Setup tab provides an graphical user interface that allows all data and parameters to be collected as required for the creation of viewpoints. (a) The upper part of the tab can be used to download and preprocess genome sequence and transcript annotation data for various mouse and human genome builds. (b) The middle part can be used to enter the targets for enrichment. Lists of target gene symbols can be uploaded from a text file or from the clipboard. Invalid or outdated gene symbols will be reported so they can be corrected. Alternatively, all protein-coding genes can be selected, or arbitrary genomic positions (such as GWAS hits) can be uploaded in BED6 format. (c) The lower part of the Setup tab can be used to specify parameters for probe and digest selection (Table 1 and Fig. 2) using the simple or extended approach