Dataset Information

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

ABSTRACT: Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified as a database and as a server. As a database it provides access to many processed Ribo-Seq and RNA-seq data aligned to reference transcriptomes which has been expanded considerably since its inception. Here, we focus on the server functionality of Trips-viz which also has been greatly improved. Trips-viz now enables visualisation of proteomics data from a large number of processed mass spectrometry datasets. It can be used to support translation inferred from Ribo-Seq data. Users are now able to upload a custom reference transcriptome as well as data types other than Ribo-Seq/RNA-Seq. Incorporating custom data has been streamlined with RiboGalaxy (https://ribogalaxy.ucc.ie/) integration. The other new functionality is the rapid detection of translated open reading frames (ORFs) through a simple easy to use interface. The analysis of differential expression has been also improved via integration of DESeq2 and Anota2seq in addition to a number of other improvements of existing Trips-viz features.

SUBMITTER: Kiniry SJ

PROVIDER: S-EPMC8262740 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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

Kiniry Stephen J SJ Judge Ciara E CE Michel Audrey M AM Baranov Pavel V PV

Nucleic acids research 20210701 W1

Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified as a database and as a server. As a database it provides access to many processed Ribo-Seq and RNA-seq data aligned to reference transcriptomes which has been expanded considerably since its inception. Here, we focus on the server funct ...[more]

PMID: 33950201

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Project description: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/.

Project description:BackgroundTherapists and their patients increasingly discuss digital data from social media, smartphone sensors, and other online engagements within the context of psychotherapy.ObjectiveWe examined patients' and mental health therapists' experiences and perceptions following a randomized controlled trial in which they both received regular summaries of patients' digital data (eg, dashboard) to review and discuss in session. The dashboard included data that patients consented to share from their social media posts, phone usage, and online searches.MethodsFollowing the randomized controlled trial, patient (n=56) and therapist (n=44) participants completed a debriefing survey after their study completion (from December 2021 to January 2022). Participants were asked about their experience receiving a digital data dashboard in psychotherapy via closed- and open-ended questions. We calculated descriptive statistics for closed-ended questions and conducted qualitative coding via NVivo (version 10; Lumivero) and natural language processing using the machine learning tool latent Dirichlet allocation to analyze open-ended questions.ResultsOf 100 participants, nearly half (n=48, 49%) described their experience with the dashboard as "positive," while the other half noted a "neutral" experience. Responses to the open-ended questions resulted in three thematic areas (nine subcategories): (1) dashboard experience (positive, neutral or negative, and comfortable); (2) perception of the dashboard's impact on enhancing therapy (accountability, increased awareness over time, and objectivity); and (3) dashboard refinements (additional sources, tailored content, and privacy).ConclusionsPatients reported that receiving their digital data helped them stay "accountable," while therapists indicated that the dashboard helped "tailor treatment plans." Patient and therapist surveys provided important feedback on their experience regularly discussing dashboards in psychotherapy.

Dataset Information

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

Publications

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

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