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Xin R, Feng X, Zhang H, Wang Y, Duan M, Xie T, Dong L, Yu Q, Huang L, Zhou F. Seven non-differentially expressed 'dark biomarkers' show transcriptional dysregulation in chronic lymphocytic leukemia. Per Med 2023. [PMID: 36705049 DOI: 10.2217/pme-2022-0123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aim: Transcriptional regulation is actively involved in the onset and progression of various diseases. This study used the feature-engineering approach model-based quantitative transcription regulation to quantitatively measure the correlation between mRNA and transcription factors in a reference dataset of chronic lymphocytic leukemia (CLL) transcriptomes. Methods: A comprehensive investigation of transcriptional regulation changes in CLL was conducted using 973 samples in six independent datasets. Results & conclusion: Seven mRNAs were detected to have significantly differential model-based quantitative transcription regulation values but no differential expression between CLL patients and controls. We called these genes 'dark biomarkers' because their original expression levels did not show differential changes in the CLL patients. The overlapping lncRNAs might have contributed their transcripts to the expression miscalculations of these dark biomarkers.
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Affiliation(s)
- Ruihao Xin
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China.,College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Xin Feng
- School of Science, Jilin Institute of Chemical Technology, Jilin,132000, China.,Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Hang Zhang
- College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Yueying Wang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Tunyang Xie
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Lin Dong
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Qiong Yu
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Lan Huang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
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Rasmussen SA, Hamosh A. Festschrift for Victor A. McKusick on the Centenary of his Birth: Introduction. Am J Med Genet A 2021; 185:3189-3192. [PMID: 34338430 PMCID: PMC8530865 DOI: 10.1002/ajmg.a.62441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Sonja A. Rasmussen
- Departments of Pediatrics and Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, USA
- Department of Epidemiology, University of Florida College of Public Health and Health Professions and College of Medicine, Gainesville, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
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