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

@article{citeulike:2687165, 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.}, address = {Tel Aviv University.}, author = {Linhart, Chaim and Halperin, Yonit and Shamir, Ron }, citeulike-article-id = {2687165}, doi = {10.1101/gr.076117.108}, issn = {1088-9051}, journal = {Genome research}, keywords = {discovery, motif}, month = {April}, posted-at = {2008-05-09 16:05:47}, priority = {2}, title = {Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.}, url = {http://dx.doi.org/10.1101/gr.076117.108}, year = {2008} }

TY - JOUR ID - citeulike:2687165 L3 - citeulike-article-id:2687165 TI - Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. JF - Genome research AD - Tel Aviv University. SN - 1088-9051 N2 - 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. KW - discovery KW - motif AU - Linhart, Chaim AU - Halperin, Yonit AU - Shamir, Ron PY - 2008/04/14/ UR - http://dx.doi.org/10.1101/gr.076117.108 ER -