Help

Herein, we provide a quick step-by-step instruction on how to easily use this database.

Overview

RPFdb stands for Ribosome Profiling (RPF) Database, which is a comprehensive resource of ribosome profiling data. Ribosome profiling was first introduced by Nicholas T. Ingolia & Jonathan S. Weissman. Several excellent reviews on ribosome profiling can be found here, including Nicholas T. Ingolia, 2014, Gloria A. Brar & Jonathan S. Weissman, 2015 and Nicholas T. Ingolia, 2016. The latest version, updated on 01, June, 2018, contains 2884 samples from 293 studies for 29 species. Please check this website often as we will frequently add newly published studies.

The main sections of this website are Home, Study browser, ORF browser, Search and Download. The Navigation bar on the right provides a quick access to the help file of each section.

Home

The Home page provides three main functions: (1) Updates on the website; (2) Quick search of RPF information of a gene and (3) Quick browse of RPF studies.

Browse

(I) Study browser page provides: (1) Meta information of the study, including abstract of study, tissue or cell source, treatment for RPF experiment, and reference genome for alignment; (2) The top 200 most translated genes. In addition, the whole RPKM table of the study is also downloadable; (3) Plots showing overall statistics of each sample, including the numbers and fraction of mapped and unmapped reads in each sample, and statistics of RPKM on different genomic regions of each sample, including 5’UTR, CDS, 3’UTR and gene.

(II) ORF browser page provides: (1) ORF Metatable and (2) More detailed information about actively translated ORFs identified by ribosome profiling. By selecting species--> study--> condition, it will displays table information of actively translated ORFs. The filtering options will allow you to refine your results further.

Search

This page provides two ways to query the database: (I) search gene; (II) search study.

(I) Search gene: by selecting a species and entering a gene name or ensemble ID in the search box of the search page (also appears in the home page), the output shows the genome information of this gene from all the samples for the selected species, including RPKM of the gene and RPKM of the 5’UTR, CDS and 3’UTR regions. The JBrowse icon provides hyperlink to a genome browser, which query and visualize context-specific RPF data.

(II) Search study: users can search studies by keywords. This feature is useful to retrieve data set from curated studies in the database.

Download

Download page also has search function so that users can quickly find out datasets of interest for download. In addition, we also support the Application Programming Interface (API), which allows developers to obtain the analysis result from RPFdb by using a HTTP client. For example, the search result of gene THI1 in Arabidopsis can be returned by using the URL http://sysbio.gzzoc.com/rpfdb/geneExpression.php?gene=THI1&species=Arabidopsis. Besides, both gene sysmol and Ensembl ID can be used as query keys.

Processing pipeline

The reference genomes for alignment are listed as follows:

Species Abbreviation Reference Link

Contact

If you have any further questions or comments, please don't hesitate to contact us.

Zhi Xie: xiezhi@gmail.com
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China

Hongwei Wang: bioccwhw@126.com
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China