RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling. Academic Article uri icon


  • 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.

published proceedings

  • Nucleic Acids Res

altmetric score

  • 1.5

author list (cited authors)

  • Xie, S., Nie, P., Wang, Y., Wang, H., Li, H., Yang, Z., ... Xie, Z.

citation count

  • 44

complete list of authors

  • Xie, Shang-Qian||Nie, Peng||Wang, Yan||Wang, Hongwei||Li, Hongyu||Yang, Zhilong||Liu, Yizhi||Ren, Jian||Xie, Zhi

publication date

  • January 2016