TY  - JOUR
A1  - Linhart, Chaim
A1  - Halperin, Yonit
A1  - Shamir, Ron
T1  - Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
Y1  - 2008/07/01 
JF  - Genome Research 
JO  - Genome Research 
DO  - 10.1101/gr.076117.108 
UR  - http://genome.cshlp.org/content/early/2008/06/03/gr.076117.108.abstract 
N2  - We present a threefold 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 predefined target set), Amadeus uncovers diverse known phenomena, as well as novel regulatory motifs. 
ER  -