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

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

doi:10.1093/nar/gkv972

Shang-Qian Xie, Hongwei Wang + Show 7 more

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https://doi.org/10.1093/nar/gkv972

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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.

Highlights

Translational control is crucial in the regulation of gene expression
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 ribosome protected mRNA fragments (RPF), RPFdb provides a genome browser to query and visualize contextspecific translated mRNA

Summary

Introduction

Translational control is crucial in the regulation of gene expression. Deregulation of translation is associated with a wide range of cancers and human diseases [1]. Hereditary hyperferritinaemia-cataract syndrome (HHCS) is an autosomal dominant disorder caused by mutations in the iron-response elements of ferritin. The mutation causes increased translation of ferritin mRNA and, elevated serum levels of ferritin. This leads to nuclear cataract, an eye disease that eventually progresses to total blindness [2]. Accurate measurement of translated mRNA is invaluable to better understand cellular functions and human diseases

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