The GWIPS‐viz Browser

Abstract

GWIPS-viz is a publicly available browser that provides Genome Wide Information on Protein Synthesis through the visualization of ribosome profiling data. Ribosome profiling (Ribo-seq) is a high-throughput technique which isolates fragments of messenger RNA that are protected by the ribosome. The alignment of the ribosome-protected fragments or footprint sequences to the corresponding reference genome and their visualization using GWIPS-viz allows for unique insights into the genome loci that are expressed as potentially translated RNA. The GWIPS-viz browser hosts both Ribo-seq data and corresponding mRNA-seq data from publicly available studies across a number of genomes, avoiding the need for computational processing on the user side. Since its initial publication in 2014, over 1885 tracks have been produced across 24 genomes. This unit describes the navigation of the GWIPS-viz genome browser, the uploading of custom tracks, and the downloading of the Ribo-seq/mRNA-seq alignment data. © 2018 by John Wiley & Sons, Inc.

Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5′UTRs

“…We took 3641 genes mentioned in the OMIM database: 1242 genes associated with dominant inheritance patterns only and 2399 associated with recessive or both inheritance patterns. We used publicly available data presented in the GWIPS-viz ( 42 ) and Trips-Viz ( 22 ) browsers to analyze these genes. At first, we checked the level of mRNA expression using the global aggregate of RNA-seq coverage data from 20 different cell types available in the GWIPS-viz.…”

“…As pure sequence-based models resulted in poor performance, we employed additional sequence-level features processed from the experimental data. Namely, we fetched total read counts for each position from ribosomal P-site identification data downloaded from the GWIPS-viz browser website ( 42 ). Read counts were capped at 5000 and then linearly scaled between 0 and 10.…”

Computational methods for ribosome profiling data analysis

“…This results in a systematic bias manifested in reduced unambiguous mappings at exon–exon junctions. This can be clearly seen in the GWIPS‐Viz browser multiregion view (Kiniry, Michel, & Baranov, ; Michel et al, ). There are splice‐aware aligners that are capable of mapping across exon–exon junctions, but the short length of ribosome footprints increases the chance of spurious mappings.…”

“…To date GWIPS‐Viz hosts Ribo‐Seq data from 23 organisms (Michel et al, ). See Kiniry, Michel, and Baranov () and Michel et al () for tutorials on how to use GWIPS‐Viz. Another large database of processed and aligned ribosome profiling data is RPFdb (Wang et al, ; S. Q. Xie et al, ).…”

Editorial: Emerging Proteins and Polypeptides Expressed by “Non-Coding RNAs”

“…As the field grows, computational resources have emerged. These include repositories of non-canonical open reading frames (such as OpenProt and sORFs used in studies published in this collection) and browsers of large ribosome profiling data collection, such as GWIPS-viz ( Kiniry et al, 2018 ; Michel et al, 2014 ) and Trips-Viz ( Kiniry et al, 2021 ; Kiniry et al, 2019 ). As such, Zaheed et al present a detailed guide on using GWIPS-Viz and Trips-Viz to explore evidence of translation of allegedly non-coding RNAs.…”