RNA splicing analysis using heterogeneous and large RNA-seq datasets.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
03 03 2023
03 03 2023
Historique:
received:
22
02
2022
accepted:
06
02
2023
entrez:
3
3
2023
pubmed:
4
3
2023
medline:
8
3
2023
Statut:
epublish
Résumé
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit increased variability compared to biological replicates, and involve thousands of unannotated splice variants resulting in increased transcriptome complexity. We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we assess the advantages of MAJIQ v2 compared to existing methods. We then apply MAJIQ v2 package to analyze differential splicing across 2,335 samples from 13 brain subregions, demonstrating its ability to offer insights into brain subregion-specific splicing regulation.
Identifiants
pubmed: 36869033
doi: 10.1038/s41467-023-36585-y
pii: 10.1038/s41467-023-36585-y
pmc: PMC9984406
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1230Subventions
Organisme : NIA NIH HHS
ID : R01 AG046544
Pays : United States
Organisme : NHLBI NIH HHS
ID : F31 HL162546
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM128096
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008216
Pays : United States
Organisme : NLM NIH HHS
ID : R01 LM013437
Pays : United States
Organisme : NICHD NIH HHS
ID : F30 HD098803
Pays : United States
Informations de copyright
© 2023. The Author(s).
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