Microarray gene expression data are useful for identifying gene expression patterns associated with cancer outcomes; however, their high dimensionality make it difficult to extract meaningful information and accurately classify tumors. Hence, developing effective methods for reducing dimensionality while preserving relevant information is a crucial task. Hybrid-based gene selection methods are widely proposed in the gene expression analysis domain and can still be enhanced in terms of efficiency and reliability. This study proposes a new hybrid-based gene selection method, called multi-filter embedded mountain gazelle optimizer (MUL-MGO), which utilizes two filters and an embedded method to remove irrelevant genes, followed by selecting the most relevant genes using recently developed MGO algorithm. To the best of our knowledge, this is the first work to exploit MGO as a gene or feature selection method. A new version of MGO, called recursive mountain gazelle optimizer (RMGO), which implements MGO algorithm recursively to avoid local optima, minimize search space, and obtain minimum gene count without decreasing the classifier's performance, is developed. The proposed RMGO is used to develop a new hybrid gene selection method employing similar filters and embedded methods as MUL-MGO, but with a recursive MGO algorithm version. The resulting method is called multi-filter embedded recursive mountain gazelle optimizer (MUL-RMGO). Several classifiers are used for cancer classification. Accordingly, several experimental studies are performed on eight microarray gene expression datasets to demonstrate the proficiencies of MUL-MGO and MUL-RMGO methods. The experimental findings indicate the efficiency and productivity of the suggested MUL-MGO and MUL-RMGO methods for gene selection. The methods outperform cutting-edge methods in the literature, with MUL-RMGO exceeding MUL-MGO in terms of accuracy and selected gene count.
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http://dx.doi.org/10.1016/j.compbiomed.2023.107674 | DOI Listing |
Cancer Rep (Hoboken)
January 2025
Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran.
Background: Bioinformatics analysis of hepatocellular carcinoma (HCC) expression profiles can aid in understanding its molecular mechanisms and identifying new targets for diagnosis and treatment.
Aim: In this study, we analyzed expression profile datasets and miRNA expression profiles related to HCC from the GEO using R software to detect differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs).
Methods And Results: Common DEGs were identified, and a PPI network was constructed using the STRING database and Cytoscape software to identify hub genes.
Front Microbiol
December 2024
Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
Soda lakes are unique double-extreme habitats characterized by high salinity and soluble carbonate alkalinity, yet harboring rich prokaryotic life. Despite intensive microbiology studies, little is known about the identity of the soda lake hydrolytic bacteria responsible for the primary degradation of the biomass organic matter, in particular cellulose. In this study, aerobic and anaerobic enrichment cultures with three forms of native insoluble cellulose inoculated with sediments from five soda lakes in south-western Siberia resulted in the isolation of four cellulotrophic haloalkaliphilic bacteria and their four saccharolytic satellites.
View Article and Find Full Text PDFFront Genet
December 2024
School of information engineering, Jingdezhen Ceramic University, Jingdezhen, China.
The early symptoms of hepatocellular carcinoma patients are often subtle and easily overlooked. By the time patients exhibit noticeable symptoms, the disease has typically progressed to middle or late stages, missing optimal treatment opportunities. Therefore, discovering biomarkers is essential for elucidating their functions for the early diagnosis and prevention.
View Article and Find Full Text PDFAnal Cell Pathol (Amst)
December 2024
Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, No. 168 Changhai Road, Shanghai 200433, China.
Trauma and burns are leading causes of death and significant global health concerns. RNA-binding proteins (RBPs) play a crucial role in post-transcriptional gene regulation, influencing various biological processes of cellular RNAs. This study aims to review the emerging trends and key areas of research on RBPs in the context of trauma and burns.
View Article and Find Full Text PDFFront Neurosci
December 2024
National Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing, China.
Hibernation, an adaptive mechanism to extreme environmental conditions, is prevalent among mammals. Its main characteristics include reduced body temperature and metabolic rate. However, the mechanisms by which hibernating animals re-enter deep sleep during the euthermic phase to sustain hibernation remain poorly understood.
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