Identification of Nine mRNA Signatures for Sepsis Using Random Forest.
Journal
Computational and mathematical methods in medicine
ISSN: 1748-6718
Titre abrégé: Comput Math Methods Med
Pays: United States
ID NLM: 101277751
Informations de publication
Date de publication:
2022
2022
Historique:
received:
09
02
2022
accepted:
28
02
2022
entrez:
29
3
2022
pubmed:
30
3
2022
medline:
5
4
2022
Statut:
epublish
Résumé
Sepsis has high fatality rates. Early diagnosis could increase its curating rates. There were no reliable molecular biomarkers to distinguish between infected and uninfected patients currently, which limit the treatment of sepsis. To this end, we analyzed gene expression datasets from the GEO database to identify its mRNA signature. First, two gene expression datasets (GSE154918 and GSE131761) were downloaded to identify the differentially expressed genes (DEGs) using Limma package. Totally 384 common DEGs were found in three contrast groups. We found that as the condition worsens, more genes were under disorder condition. Then, random forest model was performed with expression matrix of all genes as feature and disease state as label. After which 279 genes were left. We further analyzed the functions of 279 important DEGs, and their potential biological roles mainly focused on neutrophil threshing, neutrophil activation involved in immune response, neutrophil-mediated immunity, RAGE receptor binding, long-chain fatty acid binding, specific granule, tertiary granule, and secretory granule lumen. Finally, the top nine mRNAs (MCEMP1, PSTPIP2, CD177, GCA, NDUFAF1, CLIC1, UFD1, SEPT9, and UBE2A) associated with sepsis were considered as signatures for distinguishing between sepsis and healthy controls. Based on 5-fold cross-validation and leave-one-out cross-validation, the nine mRNA signature showed very high AUC.
Identifiants
pubmed: 35345523
doi: 10.1155/2022/5650024
pmc: PMC8957445
doi:
Substances chimiques
Biomarkers
0
CLIC1 protein, human
0
Chloride Channels
0
RNA, Messenger
0
UBE2A protein, human
EC 2.3.2.23
Ubiquitin-Conjugating Enzymes
EC 2.3.2.23
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5650024Informations de copyright
Copyright © 2022 Jing Zhou et al.
Déclaration de conflit d'intérêts
The authors declare that they have no competing interests.
Références
Immunity. 2021 Nov 9;54(11):2450-2464
pubmed: 34758337
Infect Immun. 2017 May 23;85(6):
pubmed: 28373355
Biomed Res Int. 2019 Apr 9;2019:2487921
pubmed: 31093495
Brief Bioinform. 2022 Jan 17;23(1):
pubmed: 34864886
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Int J Mol Sci. 2021 Jun 10;22(12):
pubmed: 34200950
IUBMB Life. 2019 Jul;71(7):956-968
pubmed: 30883005
JAMA. 2016 Feb 23;315(8):801-10
pubmed: 26903338
Inflamm Res. 2020 Feb;69(2):179-190
pubmed: 31893303
Front Neuroinform. 2014 Feb 21;8:14
pubmed: 24600388
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Zhonghua Yi Xue Za Zhi. 2020 Oct 20;100(38):2961-2965
pubmed: 33086447
Clin Sci (Lond). 2014 Jan 1;126(1):31-9
pubmed: 24020445
Immunol Lett. 2016 Oct;178:122-30
pubmed: 27568821
J Cachexia Sarcopenia Muscle. 2016 Jun;7(3):377-87
pubmed: 27239408
Nucleic Acids Res. 2022 Jan 7;50(D1):D795-D800
pubmed: 34500458
BMC Res Notes. 2021 Feb 27;14(1):76
pubmed: 33640018
Hereditas. 2021 Apr 16;158(1):13
pubmed: 33863396
Front Immunol. 2021 Jun 28;12:585412
pubmed: 34262554
Bioinformatics. 2018 Feb 1;34(3):398-406
pubmed: 29028927
Comput Biol Med. 2021 Apr;131:104255
pubmed: 33639353
Clin Transl Med. 2021 Jun;11(6):e432
pubmed: 34185410
Comput Biol Med. 2021 Jan;128:104110
pubmed: 33227577
Mol Ther Nucleic Acids. 2020 Nov 17;23:347-354
pubmed: 33425492
Nucleic Acids Res. 2020 Jan 8;48(D1):D554-D560
pubmed: 31584099
Curr Gene Ther. 2021;21(3):207-215
pubmed: 33390136
Brief Bioinform. 2021 Jul 20;22(4):
pubmed: 33048110
Exp Ther Med. 2017 May;13(5):1689-1696
pubmed: 28565754
Nucleic Acids Res. 2022 Jan 7;50(D1):D867-D874
pubmed: 34634820
Curr Gene Ther. 2020;20(1):15-24
pubmed: 32445454
Crit Care Med. 2019 Jul;47(7):984-992
pubmed: 30889023
Comput Biol Med. 2021 Oct;137:104718
pubmed: 34481182
J Infect. 2021 Aug;83(2):147-155
pubmed: 34144116
Curr Gene Ther. 2020;20(3):223-235
pubmed: 33054705
Comput Biol Med. 2020 Dec;127:103957
pubmed: 32938540
Am J Physiol Endocrinol Metab. 2002 Sep;283(3):E482-9
pubmed: 12169441
J Int Med Res. 2018 Jan;46(1):11-21
pubmed: 28760085