A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.

@article{citeulike:1846849, abstract = {Deciphering the noncoding regulatory genome has proved a formidable challenge. Despite the wealth of available gene expression data, there currently exists no broadly applicable method for characterizing the regulatory elements that shape the rich underlying dynamics. We present a general framework for detecting such regulatory DNA and RNA motifs that relies on directly assessing the mutual information between sequence and gene expression measurements. Our approach makes minimal assumptions about the background sequence model and the mechanisms by which elements affect gene expression. This provides a versatile motif discovery framework, across all data types and genomes, with exceptional sensitivity and near-zero false-positive rates. Applications from yeast to human uncover putative and established transcription-factor binding and miRNA target sites, revealing rich diversity in their spatial configurations, pervasive co-occurrences of DNA and RNA motifs, context-dependent selection for motif avoidance, and the strong impact of posttranscriptional processes on eukaryotic transcriptomes.}, address = {Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.}, author = {Elemento, O. and Slonim, N. and Tavazoie, S. }, citeulike-article-id = {1846849}, doi = {http://dx.doi.org/10.1016/j.molcel.2007.09.027}, issn = {1097-2765}, journal = {Mol Cell}, month = {October}, number = {2}, pages = {337--350}, posted-at = {2007-12-21 06:00:28}, priority = {2}, title = {A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.}, url = {http://dx.doi.org/10.1016/j.molcel.2007.09.027}, volume = {28}, year = {2007} }

TY - JOUR ID - citeulike:1846849 L3 - citeulike-article-id:1846849 N2 - Deciphering the noncoding regulatory genome has proved a formidable challenge. Despite the wealth of available gene expression data, there currently exists no broadly applicable method for characterizing the regulatory elements that shape the rich underlying dynamics. We present a general framework for detecting such regulatory DNA and RNA motifs that relies on directly assessing the mutual information between sequence and gene expression measurements. Our approach makes minimal assumptions about the background sequence model and the mechanisms by which elements affect gene expression. This provides a versatile motif discovery framework, across all data types and genomes, with exceptional sensitivity and near-zero false-positive rates. Applications from yeast to human uncover putative and established transcription-factor binding and miRNA target sites, revealing rich diversity in their spatial configurations, pervasive co-occurrences of DNA and RNA motifs, context-dependent selection for motif avoidance, and the strong impact of posttranscriptional processes on eukaryotic transcriptomes. IS - 2 JF - Mol Cell SN - 1097-2765 AD - Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. EP - 350 TI - A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types. VL - 28 SP - 337 AU - Elemento, O AU - Slonim, N AU - Tavazoie, S PY - 2007/10/26/ UR - http://dx.doi.org/10.1016/j.molcel.2007.09.027 ER -