title: RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling.
abstract: Translational control is crucial in the regulation of gene expression and deregulation of translation is associated with a wide range of cancers and human diseases. Ribosome profiling is a technique that provides genome wide information of mRNA in translation based on deep sequencing of ribosome protected mRNA fragments (RPF). RPFdb is a comprehensive resource for hosting, analyzing and visualizing RPF data, available at www.rpfdb.org or http://sysbio.sysu.edu.cn/rpfdb/index.html. The current version of database contains 777 samples from 82 studies in 8 species, processed and reanalyzed by a unified pipeline. There are two ways to query the database: by keywords of studies or by genes. The outputs are presented in three levels. (i) Study level: including meta information of studies and reprocessed data for gene expression of translated mRNAs; (ii) Sample level: including global perspective of translated mRNA and a list of the most translated mRNA of each sample from a study; (iii) Gene level: including normalized sequence counts of translated mRNA on different genomic location of a gene from multiple samples and studies. To explore rich information provided by RPF, RPFdb also provides a genome browser to query and visualize context-specific translated mRNA. Overall our database provides a simple way to search, analyze, compare, visualize and download RPF data sets.
authors.affiliation: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China Scientific Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510000, China.
authors.forename: Shang-Qian
authors.initials: SQ
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Nie
authors.affiliation: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Li
authors.affiliation: Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China yizhi_liu@aliyun.com.
authors.forename: Yizhi
authors.initials: Y
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China renjian.sysu@gmail.com.
authors.forename: Jian
authors.initials: J
authors.lastname: Ren
authors.affiliation: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China Scientific Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510000, China xiezhi@gmail.com.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Xie
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D012333:RNA, Messenger