Determination of target genes for classified molecular subtypes of triple-negative breast cancer form microarray gene expression profiling: An integrative in silico approach.
Journal
Indian journal of pathology & microbiology
ISSN: 0974-5130
Titre abrégé: Indian J Pathol Microbiol
Pays: India
ID NLM: 7605904
Informations de publication
Date de publication:
25 Mar 2024
25 Mar 2024
Historique:
received:
20
04
2022
accepted:
02
01
2023
medline:
8
5
2024
pubmed:
8
5
2024
entrez:
8
5
2024
Statut:
aheadofprint
Résumé
Highly heterogeneous triple-negative breast cancer (TNBC) has tough clinical features, which were gradually solving and improving in diagnosis by the molecular subtyping of TNBC. Presently, this study was focused on analyzing the genetic makeup of TNBC subtypes. This study explored the MicroArray expression profiling of differentially expressed genes in molecular subtypes BL1, BL2, IM, luminal androgen receptor, M, and mesenchymal stem-like of TNBC by analyzing the Gene Expression Omnibus dataset GSE167213. Various gene ontologies-based protein-protein interaction (PPI) networks were subtyped TNBC genes. The effect of genetic alteration on TNBC cases was also interpreted. The MicroArray gene expression profiling was done through R programming and subjected to functional annotation through the database for annotation, visualization, and integrated discovery. The PPI networking of functionally associated genes was interpreted by STRING. The survival analysis was done through cBioPortal. The t-test was used through R programming to generate the P values for a test of the significance of expressed genes. A total of 54,613 significant probes were analyzed in the TNBC MicroArray dataset. The functional PPI networks of BL1, BL2, and IM upregulated genes showed significant associations. The survival analysis of differentially expressed genes showed the significant prognostic effect of 32 upregulated genes of different subtypes on TNBC cases with genetic alterations, whereas the remaining genes showed no significant effects. The output of the present study provided significant target gene panels for different TNBC subtypes, which would add an informative genetic value to TNBC diagnosis.
Sections du résumé
BACKGROUND
BACKGROUND
Highly heterogeneous triple-negative breast cancer (TNBC) has tough clinical features, which were gradually solving and improving in diagnosis by the molecular subtyping of TNBC.
AIM
OBJECTIVE
Presently, this study was focused on analyzing the genetic makeup of TNBC subtypes.
SETTINGS AND DESIGN
METHODS
This study explored the MicroArray expression profiling of differentially expressed genes in molecular subtypes BL1, BL2, IM, luminal androgen receptor, M, and mesenchymal stem-like of TNBC by analyzing the Gene Expression Omnibus dataset GSE167213. Various gene ontologies-based protein-protein interaction (PPI) networks were subtyped TNBC genes. The effect of genetic alteration on TNBC cases was also interpreted.
MATERIALS AND METHODS
METHODS
The MicroArray gene expression profiling was done through R programming and subjected to functional annotation through the database for annotation, visualization, and integrated discovery. The PPI networking of functionally associated genes was interpreted by STRING. The survival analysis was done through cBioPortal.
STATISTICAL ANALYSIS USED
METHODS
The t-test was used through R programming to generate the P values for a test of the significance of expressed genes.
RESULTS
RESULTS
A total of 54,613 significant probes were analyzed in the TNBC MicroArray dataset. The functional PPI networks of BL1, BL2, and IM upregulated genes showed significant associations. The survival analysis of differentially expressed genes showed the significant prognostic effect of 32 upregulated genes of different subtypes on TNBC cases with genetic alterations, whereas the remaining genes showed no significant effects.
CONCLUSION
CONCLUSIONS
The output of the present study provided significant target gene panels for different TNBC subtypes, which would add an informative genetic value to TNBC diagnosis.
Identifiants
pubmed: 38718221
doi: 10.4103/ijpm.ijpm_353_22
pii: 00004270-990000000-00152
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
Copyright © 2024 Copyright: © 2024 Indian Journal of Pathology and Microbiology.