ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
24 05 2023
24 05 2023
Historique:
received:
20
10
2022
accepted:
16
05
2023
medline:
26
5
2023
pubmed:
25
5
2023
entrez:
24
5
2023
Statut:
epublish
Résumé
The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst ( www.expressanalyst.ca ), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any eukaryotic species. ExpressAnalyst contains a series of modules that cover from processing and annotation of FASTQ files to statistical and functional analysis of count tables or gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst allows researchers to obtain global expression profiles and gene-level insights from raw RNA-sequencing reads within 24 h. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-sequencing data from multiple non-model salamander species, including two that do not have a reference transcriptome.
Identifiants
pubmed: 37225696
doi: 10.1038/s41467-023-38785-y
pii: 10.1038/s41467-023-38785-y
pmc: PMC10209063
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2995Informations de copyright
© 2023. The Author(s).
Références
Nat Commun. 2023 May 24;14(1):2995
pubmed: 37225696
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Nucleic Acids Res. 2011 May;39(9):e57
pubmed: 21306991
Environ Toxicol Chem. 2021 Dec;40(12):3226-3233
pubmed: 34551147
Mar Drugs. 2019 Oct 11;17(10):
pubmed: 31614509
Nat Ecol Evol. 2018 Nov;2(11):1792-1799
pubmed: 30250158
Bioinformatics. 2012 Apr 15;28(8):1086-92
pubmed: 22368243
J Biochem. 2005 Jul;138(1):1-4
pubmed: 16046441
Curr Issues Mol Biol. 2018;27:71-88
pubmed: 28885175
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Nucleic Acids Res. 2019 Jan 8;47(D1):D330-D338
pubmed: 30395331
Mol Biol Evol. 2015 Apr;32(4):835-45
pubmed: 25739733
Genome Res. 2021 Apr;31(4):713-720
pubmed: 33731361
Nat Commun. 2016 Apr 13;7:11257
pubmed: 27071849
Brief Bioinform. 2022 Mar 10;23(2):
pubmed: 35076693
Genomics. 2019 Dec;111(6):1216-1225
pubmed: 30092345
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32761142
Gigascience. 2019 May 1;8(5):
pubmed: 31077315
Gigascience. 2012 Dec 27;1(1):18
pubmed: 23587118
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7821-6
pubmed: 12060727
Genome Res. 2010 Sep;20(9):1165-73
pubmed: 20508146
Nature. 2018 Feb 1;554(7690):50-55
pubmed: 29364872
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Nucleic Acids Res. 2016 Jan 4;44(D1):D457-62
pubmed: 26476454
Bioinformatics. 2005 Sep 15;21(18):3674-6
pubmed: 16081474
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Nucleic Acids Res. 2019 Jul 2;47(W1):W234-W241
pubmed: 30931480
Genome Biol. 2015 Jun 23;16:131
pubmed: 26100517