Journal Article

Integrative transcriptomic, proteomic, and machine learning approach to identifying feature genes of atrial fibrillation using atrial samples from patients with valvular heart disease

Liu, Qiming, Tang, Zhenwei, Liu, Yaozhong, Liu, Na, Bai, Fan

2021

Overview

Background Atrial fibrillation (AF) is the most common arrhythmia with poorly understood mechanisms. We aimed to investigate the biological mechanism of AF and to discover feature genes by analyzing multi-omics data and by applying a machine learning approach. Methods At the transcriptomic level, four microarray datasets (GSE41177, GSE79768, GSE115574, GSE14975) were downloaded from the Gene Expression Omnibus database, which included 130 available atrial samples from AF and sinus rhythm (SR) patients with valvular heart disease. Microarray meta-analysis was adopted to identified differentially expressed genes (DEGs). At the proteomic level, a qualitative and quantitative analysis of proteomics in the left atrial appendage of 18 patients (9 with AF and 9 with SR) who underwent cardiac valvular surgery was conducted. The machine learning correlation-based feature selection (CFS) method was introduced to selected feature genes of AF using the training set of 130 samples involved in the microarray meta-analysis. The Naive Bayes (NB) based classifier constructed using training set was evaluated on an independent validation test set GSE2240. Results 863 DEGs with FDR < 0.05 and 482 differentially expressed proteins (DEPs) with FDR < 0.1 and fold change > 1.2 were obtained from the transcriptomic and proteomic study, respectively. The DEGs and DEPs were then analyzed together which identified 30 biomarkers with consistent trends. Further, 10 features, including 8 upregulated genes (CD44, CHGB, FHL2, GGT5, IGFBP2, NRAP, SEPTIN6, YWHAQ) and 2 downregulated genes (TNNI1, TRDN) were selected from the 30 biomarkers through machine learning CFS method using training set. The NB based classifier constructed using the training set accurately and reliably classify AF from SR samples in the validation test set with a precision of 87.5% and AUC of 0.995. Conclusion Taken together, our present work might provide novel insights into the molecular mechanism and provide some promising diagnostic and therapeutic targets of AF.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Angiology / Arrhythmia / Arrhythmias and Electrophysiology / Atrial fibrillation / Bayesian analysis / Biomarkers / Blood Transfusion Medicine / Cardiac arrhythmia / Cardiac Surgery / Cardiology / Cardiovascular disease / Cardiovascular research / CD44 antigen / Coronary artery disease / Datasets / Diagnosis / DNA microarrays / Feature gene / Feature selection / FHL2 protein / Fibrillation / Gene expression / Genetic aspects / Genomes / Heart diseases / Heart surgery / Heart valve diseases / Insulin-like growth factor-binding protein 2 / Internal Medicine / Learning algorithms / Machine learning / Medicine / Medicine & Public Health / Meta-analysis / Methods / Proteomic / Proteomics / Research Article / Sample size / Scientific imaging / Software / Surgery / Therapeutic targets / Transcriptomic