Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.
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.
Linhart
Chaim
C
School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
Halperin
Yonit
Y
Shamir
Ron
R
D000465:Algorithms; D020816:Amino Acid Motifs / Q000235:genetics*; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D012984:Software; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
D035683:MicroRNAs; D014157:Transcription Factors