Bioinformatic Analysis of Key Genes and Pathways Related to Keloids.
Journal
BioMed research international
ISSN: 2314-6141
Titre abrégé: Biomed Res Int
Pays: United States
ID NLM: 101600173
Informations de publication
Date de publication:
2021
2021
Historique:
received:
11
08
2020
revised:
25
08
2020
accepted:
20
02
2021
entrez:
16
4
2021
pubmed:
17
4
2021
medline:
26
5
2021
Statut:
epublish
Résumé
The pathophysiology of keloids is complex, and the treatment for keloids is still an unmet medical need. Our study is aimed at identifying the hub genes among the differentially expressed genes (DEGs) between normal skin tissue and keloids and key pathways in the development of keloids. We downloaded the GSE92566 and GSE90051 microarray data, which contain normal skin tissue and keloid gene expression data. GSE92566 was treated as a discovery dataset for summarizing the significantly DEGs, and GSE90051 served as a validation dataset. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, Reactome enrichment analysis, gene set enrichment analysis, and gene set variation analysis were performed for the key functions and pathways enriched in DEGs. Moreover, we also validated the hub genes identified from the protein-protein interaction network and predicted miRNA-hub gene interactions. 117 downregulated DEGs and 204 upregulated DEGs in GSE92566 were identified. Extracellular and collagen-related pathways were prominent in upregulated DEGs, while the keratinization-related pathway was associated with downregulated DEGs. The hub genes included COL5A1, COL5A2, and SERPINH1, which were also validated in GSE90051. This study identified several hub genes and provided insights for the underlying pathways and miRNA-hub gene interactions for keloid development through bioinformatic analysis of two microarray datasets. Additionally, our results would support the development of future therapeutic strategies.
Sections du résumé
BACKGROUND
BACKGROUND
The pathophysiology of keloids is complex, and the treatment for keloids is still an unmet medical need. Our study is aimed at identifying the hub genes among the differentially expressed genes (DEGs) between normal skin tissue and keloids and key pathways in the development of keloids.
MATERIALS AND METHODS
METHODS
We downloaded the GSE92566 and GSE90051 microarray data, which contain normal skin tissue and keloid gene expression data. GSE92566 was treated as a discovery dataset for summarizing the significantly DEGs, and GSE90051 served as a validation dataset. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, Reactome enrichment analysis, gene set enrichment analysis, and gene set variation analysis were performed for the key functions and pathways enriched in DEGs. Moreover, we also validated the hub genes identified from the protein-protein interaction network and predicted miRNA-hub gene interactions.
RESULTS
RESULTS
117 downregulated DEGs and 204 upregulated DEGs in GSE92566 were identified. Extracellular and collagen-related pathways were prominent in upregulated DEGs, while the keratinization-related pathway was associated with downregulated DEGs. The hub genes included COL5A1, COL5A2, and SERPINH1, which were also validated in GSE90051.
CONCLUSION
CONCLUSIONS
This study identified several hub genes and provided insights for the underlying pathways and miRNA-hub gene interactions for keloid development through bioinformatic analysis of two microarray datasets. Additionally, our results would support the development of future therapeutic strategies.
Identifiants
pubmed: 33860039
doi: 10.1155/2021/5897907
pmc: PMC8009712
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5897907Informations de copyright
Copyright © 2021 Siwei Bi et al.
Déclaration de conflit d'intérêts
The authors report no conflict of interest.
Références
Am J Dermatopathol. 2004 Oct;26(5):379-84
pubmed: 15365369
J Cell Mol Med. 2018 Feb;22(2):1224-1235
pubmed: 29239102
Biomed Pharmacother. 2020 Sep;129:110287
pubmed: 32540643
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Semin Cell Dev Biol. 2017 Feb;62:142-151
pubmed: 27838364
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Blood. 2010 Oct 7;116(14):2608-15
pubmed: 20570858
Cell Cycle. 2019 Aug;18(16):1849-1867
pubmed: 31258024
Arch Dermatol Res. 2014 Nov;306(9):803-8
pubmed: 25081927
Nucleic Acids Res. 2018 Jan 4;46(D1):D239-D245
pubmed: 29156006
J Hum Genet. 2016 Dec;61(12):985-993
pubmed: 27488440
Scars Burn Heal. 2019 Aug 19;5:2059513119868659
pubmed: 31452957
Clin Exp Dermatol. 2016 Jun;41(4):341-5
pubmed: 26566758
Exp Dermatol. 2017 Aug;26(8):721-727
pubmed: 27943413
Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52
pubmed: 25352553
Wound Repair Regen. 2013 Jul-Aug;21(4):530-44
pubmed: 23815228
Nucleic Acids Res. 2020 Jan 8;48(D1):D148-D154
pubmed: 31647101
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
pubmed: 16381927
Int J Mol Sci. 2017 Mar 10;18(3):
pubmed: 28287424
JPRAS Open. 2019 Dec;22:44-54
pubmed: 32051841
Bioinformatics. 2010 Oct 1;26(19):2363-7
pubmed: 20688976
Aging (Albany NY). 2020 Feb 24;12(4):3574-3593
pubmed: 32091407
Stat Med. 2006 Sep 30;25(18):3174-89
pubmed: 16345048
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Clin Genet. 2018 Apr;93(4):936-937
pubmed: 29250776
J Burn Care Res. 2019 Oct 16;40(6):809-817
pubmed: 31184708
J Invest Dermatol. 2019 May;139(5):1073-1081
pubmed: 30472058
Br J Dermatol. 2015 Sep;173(3):852-4
pubmed: 25833201
Arch Dermatol Res. 2015 Mar;307(2):109-14
pubmed: 25266787
Arch Dermatol Res. 2010 Jul;302(5):319-39
pubmed: 20130896
Bioinformatics. 2007 Jul 15;23(14):1846-7
pubmed: 17496320
Histol Histopathol. 2015 Sep;30(9):1033-57
pubmed: 25900252
Orphanet J Rare Dis. 2013 Apr 12;8:58
pubmed: 23587214
BMC Bioinformatics. 2013 Jan 16;14:7
pubmed: 23323831
J Invest Dermatol. 2018 Jan;138(1):208-218
pubmed: 28899682
Biomed Res Int. 2016;2016:5893481
pubmed: 28101509
Nat Methods. 2017 Jan;14(1):61-64
pubmed: 27892958
J Invest Dermatol. 2018 Dec;138(12):2690-2693
pubmed: 29870686
Am J Transl Res. 2016 Aug 15;8(8):3460-70
pubmed: 27648136
Am J Hum Genet. 2010 Mar 12;86(3):389-98
pubmed: 20188343
Nucleic Acids Res. 2009 Jan;37(Database issue):D105-10
pubmed: 18996891
Am J Cancer Res. 2016 Jun 01;6(6):1358-70
pubmed: 27429849
Nat Commun. 2019 Apr 3;10(1):1523
pubmed: 30944313
Dermatol Surg. 2017 Jan;43 Suppl 1:S3-S18
pubmed: 27347634
BMC Bioinformatics. 2003 Jan 13;4:2
pubmed: 12525261
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Int J Urol. 2018 Nov;25(11):953-965
pubmed: 30153702
Nature. 1953 Apr 25;171(4356):737-8
pubmed: 13054692
Int J Mol Sci. 2018 Mar 02;19(3):
pubmed: 29498630
Genome Med. 2016 Dec 13;8(1):129
pubmed: 27964755
Nucleic Acids Res. 2016 Jul 8;44(W1):W135-41
pubmed: 27105848
Nat Methods. 2016 Nov 29;13(12):966-967
pubmed: 27898060
Mol Ther Nucleic Acids. 2019 Jun 7;16:616-625
pubmed: 31100613
J Investig Dermatol Symp Proc. 2017 Oct;18(2):S50-S53
pubmed: 28941494