Screenshots of the Genomic HyperBrowser. (a) Screenshot of the main interface for selecting analysis options. The selections for the example relating H3K27me3 BLOCs to SINE repeats have been pre-selected. In the interface, the user selects a genome build followed by two tracks. A list of relevant investigations is then presented, based on the genomic types of the two tracks. After selecting an investigation, the interface presents the user with a choice of null models, alternative hypotheses and other relevant options. (b) Screenshot of the results of the analysis. The question asked by the user is presented at the top, in this case: 'Are 'MEFB1 (BLOC segments)' overlapping 'SINE (Repeating elements)' more than expected by chance?' A first, simplistic answer is then presented: 'No support from data for this conclusion in any bin'. A more precise answer follows, detailing any global P-values, a summary of local FDR-corrected P-values, the particular set of null and alternative hypotheses tested, in addition to a legend of the test statistic that has been used. Further links to a PDF file containing the statistical details of the test, and to more detailed tables of relevant statistics for both the global and the local analysis are also included. The global result table also includes links to plots and export opportunities for the individual statistics.
Sandve et al. Genome Biology 2010 11:R121 doi:10.1186/gb-2010-11-12-r121