Screenshot of Amadeus. The left panel controls the input parameters (organism, target set, promoter region, scores, etc.). Here, Amadeus was executed on the set of genes expressed in G2 and G2/M phases of the human cell cycle (Whitfield et al. 2002). The top-scoring motif shown in the output panel on the right is CHR (cell-cycle genes homology region), a cis-regulatory element that was experimentally found in promoters of several G2/M genes (Zhu et al. 2004), and is not represented in TRANSFAC; the second motif is CCAAT-box (NF-Y). For each motif discovered, the output also lists similar patterns from TRANSFAC, information on the localization of its occurrences, and additional statistics. In agreement with recent studies (Linhart et al. 2005; Tabach et al. 2005), the motif-pairs analysis in Amadeus reports the de novo found CHR and NF-Y motifs as a cis-regulatory module that is highly specific to the G2 and G2/M cell-cycle phases (Supplemental Fig. 1). A screenshot with additional graphical features is shown in Supplemental Figure 2.
