HRPDviewer: human ribosome profiling data viewer

Abstract

Translational regulation plays an important role in protein synthesis. Dysregulation of translation causes abnormal cell physiology and leads to diseases such as inflammatory disorders and cancers. An emerging technique, called ribosome profiling (ribo-seq), was developed to capture a snapshot of translation. It is based on deep sequencing of ribosome-protected mRNA fragments. A lot of ribo-seq data have been generated in various studies, so databases are needed for depositing and visualizing the published ribo-seq data. Nowadays, GWIPS-viz, RPFdb and TranslatomeDB are the three largest databases developed for this purpose. However, two challenges remain to be addressed. First, GWIPS-viz and RPFdb databases align the published ribo-seq data to the genome. Since ribo-seq data aim to reveal the actively translated mRNA transcripts, there are advantages of aligning ribo-req data to the transcriptome over the genome. Second, TranslatomeDB does not provide any visualization and the other two databases only provide visualization of the ribo-seq data around a specific genomic location, while simultaneous visualization of the ribo-seq data on multiple mRNA transcripts produced from the same gene or different genes is desired. To address these two challenges, we developed the Human Ribosome Profiling Data viewer (HRPDviewer). HRPDviewer (i) contains 610 published human ribo-seq datasets from Gene Expression Omnibus, (ii) aligns the ribo-seq data to the transcriptome and (iii) provides visualization of the ribo-seq data on the selected mRNA transcripts. Using HRPDviewer, researchers can compare the ribosome binding patterns of multiple mRNA transcripts from the same gene or different genes to gain an accurate understanding of protein synthesis in human cells. We believe that HRPDviewer is a useful resource for researchers to study translational regulation in human.Database URL: http://cosbi4.ee.ncku.edu.tw/HRPDviewer/ or http://cosbi5.ee.ncku.edu.tw/HRPDviewer/

Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans

“…Diverse ribosome profiling sequencing results are fragmentary in the literature. Recently, a database called HPRDviewer ( 41 ) is constructed to deposit comprehensive human ribosome profiling datasets. In Human IRES Atlas, the conditional ribosome profiling results performed under the stressed and normal conditions are shown.…”

“…To integrate the ribosome profiling results, we first used the NCBI SRA Toolkit to download the sequencing results and then transformed the results into the fastq format. We followed the peak calling procedure used in the HRPDviewer ( 41 ) to obtain the transcript nucleotide-level reads for both conditions. First, the adaptor linker sequences or poly-(A) tails of the short reads are trimmed by Cutadapt ( 42 ).…”

Tissue- and development-stage–specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples

“…The ribosome profiling databases HRPDviewer ( 34 ) and RPFdb ( 35 ) were searched to identify human and rodent datasets with translation data in multiple tissue/cell-types, and the following RNA-seq (i.e. mRNA expression) data and ribosome profiling (i.e.…”

Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data

“…Instead, a more detailed comparison was made to other online databases which either provide pre-processed data or provide an easy way to process Ribo-Seq data which does not require computational expertise. These tools include RiboToolKit ( 7 ), SmProt ( 45 ), HRPDViewer ( 46 ), TranslatomeDB ( 15 ), RiboViz ( 47 ), RPFdb ( 12 ), OpenProt ( 13 ), GWIPS-Viz ( 48 ), RiboGalaxy ( 6 ) and RiboStreamR ( 49 ). The features of these tools are listed in Table 1 .…”