vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis.

Algorithms Phenotype Software Internet Computational Biology / instrumentation Data Visualization

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
05 07 2023
Historique:
accepted: 01 05 2023
revised: 13 04 2023
received: 12 03 2023
medline: 6 7 2023
pubmed: 9 5 2023
entrez: 9 5 2023
Statut: ppublish

Résumé

Gene-set analysis (GSA) dominates the functional interpretation of omics data and downstream hypothesis generation. Despite its ability to summarise thousands of measurements into semantically interpretable components, GSA often results in hundreds of significantly enriched gene-sets. However, summarisation and effective visualisation of GSA results to facilitate hypothesis generation is still lacking. While some webservers provide gene-set visualization tools, there is still a need for tools that can effectively summarize and guide exploration of GSA results. To enable versatility, webservers accept gene lists as input, however, none provide end-to-end solutions for emerging data types such as single-cell and spatial omics. Here, we present vissE.Cloud, a webserver for end-to-end gene-set analysis, offering gene-set summarisation and highly interactive visualisation. vissE.Cloud uses algorithms from our earlier R package vissE to summarise GSA results by identifying biological themes. We maintain versatility by allowing analysis of gene lists, as well as, analysis of raw single-cell and spatial omics data, including CosMx and Xenium data, making vissE.Cloud the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data. Structuring the results hierarchically allows swift interactive investigations of results at the gene, gene-set, and clusters level. vissE.Cloud is freely available at https://www.vissE.Cloud.

Identifiants

DOI: 10.1093/nar/gkad337 PMID: 37158226 PMC: PMC10320187
pubmed: 37158226
pii: 7157520
doi: 10.1093/nar/gkad337
pmc: PMC10320187
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

W593-W600

Informations de copyright

© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

Références

Nat Biotechnol. 2022 Dec;40(12):1794-1806
pubmed: 36203011
NAR Genom Bioinform. 2023 Mar 03;5(1):lqad024
pubmed: 36879897
Nucleic Acids Res. 2019 Jul 2;47(W1):W199-W205
pubmed: 31114916
Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63
pubmed: 24234451
Nucleic Acids Res. 2022 Jan 7;50(D1):D687-D692
pubmed: 34788843
Nat Methods. 2017 Nov;14(11):1083-1086
pubmed: 28991892
Bioinformatics. 2008 Feb 1;24(3):374-82
pubmed: 18204063
Nat Methods. 2020 Feb;17(2):137-145
pubmed: 31792435
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
F1000Res. 2016 Aug 31;5:2122
pubmed: 27909575
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7
pubmed: 27141961
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
BMC Bioinformatics. 2020 Oct 7;21(1):443
pubmed: 33028195
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W305-11
pubmed: 19465376
Innovation (Camb). 2021 Jul 01;2(3):100141
pubmed: 34557778
BMC Bioinformatics. 2018 Nov 6;19(1):404
pubmed: 30400809
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
Nucleic Acids Res. 2019 Dec 2;47(21):e133
pubmed: 31294801
PLoS One. 2010 Nov 15;5(11):e13984
pubmed: 21085593
Nucleic Acids Res. 2019 Jul 2;47(W1):W191-W198
pubmed: 31066453
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Front Mol Biosci. 2021 Sep 16;8:716544
pubmed: 34604304
PLoS One. 2011;6(7):e21800
pubmed: 21789182
F1000Res. 2016 Jun 20;5:1438
pubmed: 27508061
Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334
pubmed: 33290552
Cell Syst. 2015 Dec 23;1(6):417-425
pubmed: 26771021
Nucleic Acids Res. 2009 Jan;37(1):1-13
pubmed: 19033363
Nat Protoc. 2019 Mar;14(3):703-721
pubmed: 30804569
Bioinformatics. 2017 Apr 15;33(8):1179-1186
pubmed: 28088763
Nat Protoc. 2016 Dec;11(12):2301-2319
pubmed: 27809316
BMC Bioinformatics. 2020 Jun 29;21(1):267
pubmed: 32600310
Genome Biol. 2016 Apr 27;17:75
pubmed: 27122128
Nat Methods. 2020 Jan;17(1):41-44
pubmed: 31768060
PLoS Comput Biol. 2012;8(2):e1002375
pubmed: 22383865
Nucleic Acids Res. 2020 Nov 4;48(19):e113
pubmed: 32997146
Nat Commun. 2019 Apr 3;10(1):1523
pubmed: 30944313

Auteurs

Ahmed Mohamed (A)

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.
Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
Colonial Foundation Healthy Ageing Centre, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.
ORCID: 0000-0001-6507-5300

Dharmesh D Bhuva (DD)

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.
Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.
ORCID: 0000-0002-6398-9157

Sam Lee (S)

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.
Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.

Ning Liu (N)

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.
Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.

Chin Wee Tan (CW)

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.
Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia.

Melissa J Davis (MJ)

Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia.
Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.
Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia.
Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia.
ORCID: 0000-0003-4864-7033

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Classifications MeSH

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