ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery.

Mobile Applications High-Throughput Nucleotide Sequencing Biomedical Research Gene Ontology Sequence Analysis, RNA
Biomarkers Differential expression GSEA Gene ontology R Shiny RNA-Seq

Journal

BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194

Informations de publication

Date de publication:
29 Jul 2023
Historique:
received: 13 11 2020
accepted: 18 07 2023
medline: 31 7 2023
pubmed: 30 7 2023
entrez: 29 7 2023
Statut: epublish

Résumé

The growing power and ever decreasing cost of RNA sequencing (RNA-Seq) technologies have resulted in an explosion of RNA-Seq data production. Comparing gene expression values within RNA-Seq datasets is relatively easy for many interdisciplinary biomedical researchers; however, user-friendly software applications increase the ability of biologists to efficiently explore available datasets. Here, we describe ROGUE (RNA-Seq Ontology Graphic User Environment, https://marisshiny. chop.edu/ROGUE/ ), a user-friendly R Shiny application that allows a biologist to perform differentially expressed gene analysis, gene ontology and pathway enrichment analysis, potential biomarker identification, and advanced statistical analyses. We use ROGUE to identify potential biomarkers and show unique enriched pathways between various immune cells. User-friendly tools for the analysis of next generation sequencing data, such as ROGUE, will allow biologists to efficiently explore their datasets, discover expression patterns, and advance their research by allowing them to develop and test hypotheses.

Sections du résumé

BACKGROUND BACKGROUND
The growing power and ever decreasing cost of RNA sequencing (RNA-Seq) technologies have resulted in an explosion of RNA-Seq data production. Comparing gene expression values within RNA-Seq datasets is relatively easy for many interdisciplinary biomedical researchers; however, user-friendly software applications increase the ability of biologists to efficiently explore available datasets.
RESULTS RESULTS
Here, we describe ROGUE (RNA-Seq Ontology Graphic User Environment, https://marisshiny.
RESEARCH METHODS
chop.edu/ROGUE/ ), a user-friendly R Shiny application that allows a biologist to perform differentially expressed gene analysis, gene ontology and pathway enrichment analysis, potential biomarker identification, and advanced statistical analyses. We use ROGUE to identify potential biomarkers and show unique enriched pathways between various immune cells.
CONCLUSIONS CONCLUSIONS
User-friendly tools for the analysis of next generation sequencing data, such as ROGUE, will allow biologists to efficiently explore their datasets, discover expression patterns, and advance their research by allowing them to develop and test hypotheses.

Identifiants

DOI: 10.1186/s12859-023-05420-y PMID: 37516886 PMC: PMC10386769
pubmed: 37516886
doi: 10.1186/s12859-023-05420-y
pii: 10.1186/s12859-023-05420-y
pmc: PMC10386769
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

303

Subventions

Organisme : NCI NIH HHS
ID : U54 CA232568
Pays : United States
Organisme : NCI NIH HHS
ID : R35 CA220500
Pays : United States
Organisme : NCI NIH HHS
ID : P01 CA217959
Pays : United States

Informations de copyright

© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.

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Auteurs

Alvin Farrel (A)

Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA. farrela@chop.edu.
Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA. farrela@chop.edu.
Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA. farrela@chop.edu.
Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. farrela@chop.edu.
ORCID: 0000-0003-1087-9840

Peng Li (P)

Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.

Sharon Veenbergen (S)

Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
Laboratory of Pediatric Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands.
Laboratory of Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands.

Khushbu Patel (K)

Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.

John M Maris (JM)

Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.

Warren J Leonard (WJ)

Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA. wjl@helix.nih.gov.
Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA. wjl@helix.nih.gov.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Applications mobiles › ROGUE: an R Shiny app for RNA sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › ROGUE: an R Shiny app for RNA sequencing...
questionsmedicales.fr › Disciplines des sciences naturelles › Science › Recherche › Recherche biomédicale › ROGUE: an R Shiny app for RNA sequencing...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Vocabulaire contrôlé › Ontologies biologiques › Gene Ontology › ROGUE: an R Shiny app for RNA sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › ROGUE: an R Shiny app for RNA sequencing...