Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
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↵1 These authors contributed equally to this work.
Abstract
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.
Footnotes
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↵2 Corresponding author.
↵2 E-mail rshamir{at}tau.ac.il; fax 972-3-640-5384.
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[Supplemental material is available online at www.genome.org. The Amadeus software is available at http://acgt.cs.tau.ac.il/amadeus.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.076117.108.
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- Received January 8, 2008.
- Accepted April 2, 2008.
- Copyright © 2008, Cold Spring Harbor Laboratory Press
