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Machine learning assisted analysis of breast cancer gene expression profiles reveals novel potential prognostic biomarkers for triple-negative breast cancer.

التفاصيل البيبلوغرافية
العنوان: Machine learning assisted analysis of breast cancer gene expression profiles reveals novel potential prognostic biomarkers for triple-negative breast cancer.
المؤلفون: Thalor A; Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India., Kumar Joon H; Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.; Regional Centre for Biotechnology, Faridabad 121001, Haryana, India., Singh G; Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India., Roy S; Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India., Gupta D; Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
المصدر: Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2022 Mar 24; Vol. 20, pp. 1618-1631. Date of Electronic Publication: 2022 Mar 24 (Print Publication: 2022).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology Country of Publication: Netherlands NLM ID: 101585369 Publication Model: eCollection Cited Medium: Print ISSN: 2001-0370 (Print) Linking ISSN: 20010370 NLM ISO Abbreviation: Comput Struct Biotechnol J Subsets: PubMed not MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology
Original Publication: Gothenburg, Sweden : Research Network of Computational and Structural Biotechnology
مستخلص: Tumor heterogeneity and the unclear metastasis mechanisms are the leading cause for the unavailability of effective targeted therapy for Triple-negative breast cancer (TNBC), a breast cancer (BrCa) subtype characterized by high mortality and high frequency of distant metastasis cases. The identification of prognostic biomarker can improve prognosis and personalized treatment regimes. Herein, we collected gene expression datasets representing TNBC and Non-TNBC BrCa. From the complete dataset, a subset reflecting solely known cancer driver genes was also constructed. Recursive Feature Elimination (RFE) was employed to identify top 20, 25, 30, 35, 40, 45, and 50 gene signatures that differentiate TNBC from the other BrCa subtypes. Five machine learning algorithms were employed on these selected features and on the basis of model performance evaluation, it was found that for the complete and driver dataset, XGBoost performs the best for a subset of 25 and 20 genes, respectively. Out of these 45 genes from the two datasets, 34 genes were found to be differentially regulated. The Kaplan-Meier (KM) analysis for Distant Metastasis Free Survival (DMFS) of these 34 differentially regulated genes revealed four genes, out of which two are novel that could be potential prognostic genes ( POU2AF1 and S100B ). Finally, interactome and pathway enrichment analyses were carried out to investigate the functional role of the identified potential prognostic genes in TNBC. These genes are associated with MAPK, PI3-AkT, Wnt, TGF-β, and other signal transduction pathways, pivotal in metastasis cascade. These gene signatures can provide novel molecular-level insights into metastasis.
Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(© 2022 The Authors.)
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فهرسة مساهمة: Keywords: AUC, Area under the ROC curve; BrCa, Breast cancer; COSMIC, The catalogue of somatic mutations in cancer; CX-25, Complete XgBoost top 25; DE, Differential Expression; DMFS, Distasnt metastasis free survival; DX-20, Driver XgBoost top 20; Differential gene expression; Distant-metastasis free survival; EMT, Epithelial to mesenchymal transition; ER, Oestrogen Receptor; FDR, False discovery rate; GEO, Gene expression omnibous; HER2, Human epidermal growth factor receptor 2; KM, Kaplan Meier; ML, Machine learning; NSCLC, Non small cell lung carcinoma; OS, Overall survival; PCA, Principal component analysis; POU2AF1; PR, Progesterone receptor; Prognostic gene signatures; RF, Random forest; RFE, Recursive feature elimination; ROC, Receiver operating characteristics curve; S100B; SVM, Support vector machine; TNBC; TNBC, Triple negative breast cancer; kNN, k Nearest neighbors
تواريخ الأحداث: Date Created: 20220425 Latest Revision: 20220716
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC9014315
DOI: 10.1016/j.csbj.2022.03.019
PMID: 35465161
قاعدة البيانات: MEDLINE
الوصف
تدمد:2001-0370
DOI:10.1016/j.csbj.2022.03.019