Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

Abstract

We present a three-fold contribution to the computational task of motif discovery, a key component in the effort of delineating the regulatory map of a genome: 1) We constructed a comprehensive large-scale, publicly-available compendium of transcription factor and microRNA target gene sets derived from diverse high-throughput experiments in several metazoans. We used the compendium as a benchmark for motif discovery tools. 2) We developed Amadeus, a highly efficient, user-friendly software platform for genome-scale detection of novel motifs, applicable to a wide range of motif discovery tasks. Amadeus improves upon extant tools in terms of accuracy, running time, output information and ease-of-use, and is the only program that attained a high success rate on the metazoan compendium. 3) We demonstrate that by searching for motifs based on their genome-wide localization or chromosomal distributions (without using a pre-defined target set), Amadeus uncovers diverse known phenomena, as well as novel regulatory motifs.

• benchmark for motif finding
• motif discovery
• transcription factor binding sites