@article{e3b2b6c23b894c0d936e255efd096fb7,
title = "Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites",
abstract = "Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites. Such combinatorial clustering of RBPs helps interpret CLIP-seq data and suggests functional RNA regulatory elements. Furthermore, we validate two RBP-RBP interactions in cell lines. Our approach links proteins and RNA motifs known to possess similar biochemical and cellular properties and can, when used in conjunction with additional experimental data, identify high-confidence RBP groups and their associated RNA regulatory elements.",
keywords = "CLIP-seq, Non-negative matrix factorization, RBPgroup, RNA-binding protein",
author = "Li, {Yang Eric} and Mu Xiao and Binbin Shi and Yang, {Yu Cheng T.} and Dong Wang and Fei Wang and Marco Marcia and Lu, {Zhi John}",
note = "Funding Information: This study was supported by National Key Research and Development Plan of China (2016YFA0500803), National Natural Science Foundation of China (31522030, 31771461 and 31371417), and Tsinghua University Initiative Scientific Research Program (2014z21045). This study was also supported by Beijing Advanced Innovation Center for Structural Biology and Computing Platform of National Protein Facilities (Tsinghua University). Work in the Marcia lab is partly funded by the Agence Nationale de la Recherche (ANR-15-CE11-0003-01) and by the Agence Nationale de Recherche sur le Sida et les h{\'e}patites virales (ANRS) (ECTZ18552) and uses the platforms of the Grenoble Instruct Center (ISBG: UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB). Publisher Copyright: {\textcopyright} 2017 The Author(s).",
year = "2017",
month = sep,
day = "8",
doi = "10.1186/s13059-017-1298-8",
language = "English",
volume = "18",
journal = "Genome biology",
issn = "1474-7596",
number = "1",
}