0. 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 20, June, 2024, contains 5,018 Ribo-seq samples across 496 studies, complemented by matched RNA-seq data from 2,343 samples, encompassing 34 distinct species.

The main sections of this website are Home, Study browse,Sample browse, actively translated ORF browse, Search ribosome occupancy, Search translation efficiency, Search pausing score, Download, Statistics, Resource, and Citation. The Navigation bar on the right provides a quick access to the help file of each section.

1. Home

Home page offers a comprehensive introduction, featuring convenient starting points: (1) Website updates; (2) Rapid search of RPFdb information; and (3) Efficient browsing of RPFdb information.

2. Browse

This includes Study browse and Sample browse.

(I) Study browse page offers meta-information for each study along with a convenient search button to help you find studies of interest quickly. Move the mouse point over the details button to preview sample information.

(II) Sample browse page displays: (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.

3. ORF Catalog

Ribo-seq ORF Catalog page offers comprehensive details on actively translated ORFs identified in ribosome profiling using RibORF. 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.

4. Quantification

This includes measurements of ribosome occupancy, translation efficiency, and pausing score.

(I) Ribosome occupancy page offers measurements of ribosome occupancy. 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) Translation efficiency page offers measurements of translation efficiency by comparing ribo-seq data to RNA-seq data. 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 translation efficiency values of this gene from all the samples for the selected species.

(III) Pausing score page provides context-specific pausing scores for each triplet amino acid (AA) within each sample. The pausing score for each triplet amino acid is defined as the sum of ribosome density covering this tri-AA motif. These pausing scores can help identify tri-AA motifs that exhibit higher ribosome enrichment.

5. 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 SNOR77 in A.thaliana can be returned by using the URL http://sysbio.gzzoc.com/rpfdb/geneExpression.php?gene=SNOR77&species=Athaliana. Besides, both gene sysmol and Ensembl ID can be used as query keys.

6. Statistics

This page graphically compares data inclusion across different versions, and provides detailed distributions of study and sample species.

7. Resource

This page provides an overview of advances in the techniques of studying translatome and the existing computational resources for ribo-seq data. Some representative articles and tools have been provided.

8. Citation

This page provides copyright and licensing information, guidelines for citing RPFdb, and contact details.

9. Preprocessing pipeline

The reference genomes for alignment are listed as follows:

Species	Abbreviation	Reference	Link