Search region masks

The location of a search region and the motifs and modules it contains are shown in UCSC genome browser images on the search region pages. Although motif predictions were not made in coding exons and most types of repeats, the location of the search region masks were not visible in these images.

Now, the locations of masks applied to the search regions have been added to the genome browser images in the current version of the human, mouse, rat, and human Stat1 Chip-seq databases. Masked regions are coloured gray within a red search region.

Information about the mask locations is contained in the search_region_masks mySQL table. This table has been added to the following publicly accessible databases at db.cisred.org: cisred_Hsap_8_3, cisred_Hsap_Stat1_ChIP_peaks, cisred_Mmus_3_1, cisred_Rnor_1_1. (Access these databases with username 'anonymous'; no password is required.) Files containing the mySQL 'create table' statement and the data for the search_region_masks table can be downloaded from the 'Databases & Methods' section of this website.

View all cisRED news items.