How to view the peaks in the UCSC genome browser 1. Go to the UCSC genome browser, http://genome.ucsc.edu/ 2. Select "Genome Browser" link 3. Select "add custom tracks" 4. Browse to the website containing the peak-profiles. They are grouped into catalogues for each transcription factor (NRSF, SRF and Max) and again in "positive","ambigous" and "negative" peaks. Select a peak to display 5. Select "Submit". You should now get an overview with the following 5-7 tracks. - a positive strand: profile for tags mapped to positive strand (displayed in green) - b negative strand: profile for tags mapped to positive strand (displayed in red) - c combined and shifted: tag profile for the shifted and combined strand tags (displayed in blue) - d classified peak: region where a peak has been evaluated. Colours are green for true peaks, blue for ambiguos peaks and red for false peaks. If no peak has been evaluated, no track will be displayed - e classified site: Evaluated potential binding sites. Colours are green for true sites, blue for ambiguos sites and red for false sites. By clicking on a site, the pwm-score for the site (scaled from 0 to 1000) is displayed. A value of 0 means the site scored below the enrichment threshold - f background track: background tag profile for both strands combined (displayed in black) - g replicate track: replicate tag profile for the shifted and combined strand tags (displayed in blue) 6. Select "go to genome browser" to display tracks