Gene Set Analysis: Challenges, Opportunities, and Future Research.
gene expression
gene set analysis
gene set database
gene set enrichment
sensitivity
specificity
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2020
2020
Historique:
received:
01
02
2020
accepted:
29
05
2020
entrez:
23
7
2020
pubmed:
23
7
2020
medline:
23
7
2020
Statut:
epublish
Résumé
Gene set analysis methods are widely used to provide insight into high-throughput gene expression data. There are many gene set analysis methods available. These methods rely on various assumptions and have different requirements, strengths and weaknesses. In this paper, we classify gene set analysis methods based on their components, describe the underlying requirements and assumptions for each class, and provide directions for future research in developing and evaluating gene set analysis methods.
Identifiants
pubmed: 32695141
doi: 10.3389/fgene.2020.00654
pmc: PMC7339292
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
654Informations de copyright
Copyright © 2020 Maleki, Ovens, Hogan and Kusalik.
Références
Cancer Lett. 2016 Jul 1;376(2):284-92
pubmed: 27063096
BMC Bioinformatics. 2017 May 12;18(1):256
pubmed: 28499413
Autoimmunity. 2020 Mar;53(2):102-113
pubmed: 31809599
PLoS One. 2018 Jan 25;13(1):e0191154
pubmed: 29370226
Genes (Basel). 2020 Apr 17;11(4):
pubmed: 32316383
PLoS Comput Biol. 2012;8(2):e1002375
pubmed: 22383865
Genome Biol. 2010;11(2):R23
pubmed: 20187943
BMC Bioinformatics. 2019 Mar 18;20(1):145
pubmed: 30885118
BMC Syst Biol. 2012 Jun 06;6:56
pubmed: 22672776
BMC Bioinformatics. 2007 Aug 06;8:290
pubmed: 17683603
PLoS One. 2013 Nov 15;8(11):e79217
pubmed: 24260172
Genome Res. 2007 Oct;17(10):1537-45
pubmed: 17785539
Entropy (Basel). 2020 Apr 10;22(4):
pubmed: 33286201
Source Code Biol Med. 2012 Sep 24;7(1):10
pubmed: 23006764
Bioinformatics. 2009 Nov 1;25(21):2780-6
pubmed: 19689953
Bioinformatics. 2005 Apr 1;21(7):1129-37
pubmed: 15550480
BMC Bioinformatics. 2005 Jun 08;6:144
pubmed: 15941488
Bioinformatics. 2009 Jan 1;25(1):75-82
pubmed: 18990722
Stat Methods Med Res. 2009 Dec;18(6):565-75
pubmed: 20048385
Nature. 2020 Feb;578(7795):437-443
pubmed: 32025032
Diabetes. 2002 Jun;51(6):1913-20
pubmed: 12031981
Brief Bioinform. 2016 May;17(3):393-407
pubmed: 26342128
Stat Methods Med Res. 2016 Feb;25(1):472-87
pubmed: 23070592
Genomics. 2002 Feb;79(2):266-70
pubmed: 11829497
PLoS Comput Biol. 2015 Oct 05;11(10):e1004467
pubmed: 26436655
Brief Bioinform. 2008 May;9(3):189-97
pubmed: 18202032
Nat Genet. 2004 Jul;36(7):663; author reply 663
pubmed: 15226741
Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12890-5
pubmed: 17652168
BMC Bioinformatics. 2015 Oct 22;16:334
pubmed: 26489510
Bioinformatics. 2006 Oct 1;22(19):2373-80
pubmed: 16877751
BMC Syst Biol. 2010 Sep 01;4:121
pubmed: 20809931
Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6
pubmed: 18842627
Microarrays (Basel). 2015 Oct 16;4(4):432-53
pubmed: 27600233
BMC Bioinformatics. 2017 Mar 4;18(1):151
pubmed: 28259142
Brief Bioinform. 2012 May;13(3):281-91
pubmed: 21900207
Sci Rep. 2014 Feb 13;4:4092
pubmed: 24522610
Brief Bioinform. 2021 Jan 18;22(1):545-556
pubmed: 32026945
Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56
pubmed: 25428369
Nucleic Acids Res. 2012 Jan;40(Database issue):D1060-6
pubmed: 22110038
Bioinformatics. 2007 Feb 1;23(3):306-13
pubmed: 17127676
Front Physiol. 2013 Oct 10;4:278
pubmed: 24133454
BMC Bioinformatics. 2004 Dec 09;5:193
pubmed: 15588298
Genome Biol. 2004;5(10):R80
pubmed: 15461798
Nat Genet. 2003 Jul;34(3):267-73
pubmed: 12808457
Genomics. 2003 Feb;81(2):98-104
pubmed: 12620386
Nucleic Acids Res. 2016 Jan 4;44(D1):D457-62
pubmed: 26476454
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):8961-5
pubmed: 15951424
Bioinformatics. 2007 Apr 15;23(8):980-7
pubmed: 17303618
BMC Genomics. 2010 Oct 18;11:574
pubmed: 20955544
PLoS One. 2010 Apr 20;5(4):e10247
pubmed: 20422035
Nucleic Acids Res. 2013 Jan 7;41(1):e19
pubmed: 23002139
BioData Min. 2018 May 31;11:8
pubmed: 29881462
Bioinformatics. 2004 Jan 1;20(1):93-9
pubmed: 14693814
Nucleic Acids Res. 2009 Jan;37(1):1-13
pubmed: 19033363
BMC Bioinformatics. 2009 Feb 03;10:47
pubmed: 19192285
PLoS One. 2010 Sep 17;5(9):
pubmed: 20862301
Genome Biol. 2019 Oct 9;20(1):203
pubmed: 31597578
BMC Bioinformatics. 2012 Jun 19;13:136
pubmed: 22713124
J Bioinform Comput Biol. 2019 Oct;17(5):1940010
pubmed: 31856670
Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13544-9
pubmed: 16174746
J Comput Biol. 2012 May;19(5):563-73
pubmed: 22468678
BMC Bioinformatics. 2007 Nov 07;8:431
pubmed: 17988400
J Comput Biol. 2007 Sep;14(7):961-72
pubmed: 17803373
Hum Genomics. 2019 Oct 22;13(Suppl 1):42
pubmed: 31639047
Diabetologia. 2002 Nov;45(11):1584-93
pubmed: 12436343
Brief Bioinform. 2014 Jul;15(4):504-18
pubmed: 23413432
Bioinformatics. 2007 Nov 15;23(22):3100-2
pubmed: 17890270
Cell Metab. 2019 Jul 2;30(1):190-200.e6
pubmed: 31105043
Bioinformatics. 2019 Dec 15;35(24):5146-5154
pubmed: 31165139
Nature. 2019 Jul;571(7766):505-509
pubmed: 31243369
FEBS Open Bio. 2012 Apr 17;2:76-82
pubmed: 23650583
Nucleic Acids Res. 2013 Apr;41(7):e82
pubmed: 23389952
Nature. 2019 Jan;565(7740):495-499
pubmed: 30626970
Appl Bioinformatics. 2004;3(4):261-4
pubmed: 15702958