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Pan Y, Wu L, He S, Wu J, Wang T, Zang H. Identification of hub genes in thyroid carcinoma to predict prognosis by integrated bioinformatics analysis. Bioengineered 2021; 12:2928-2940. [PMID: 34167437 PMCID: PMC8806580 DOI: 10.1080/21655979.2021.1940615] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The aim of this study was to identify hub genes closely related to the pathogenesis and prognosis of thyroid carcinoma (THCA) by integrated bioinformatics analysis. In this study, through differential gene expression analysis, 1916 and 665 differentially expressed genes (DEGs) were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, and 7 and 11 co-expressed modules were identified from the TCGA-THCA and GSE153659 datasets, respectively, by weighted gene co-expression network analysis. We identified 162 overlapping genes between the DEGs and co-expression module genes as candidate hub genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the 162 overlapping DEGs identified significant functions and pathways of THCA, such as thyroid hormone generation and metabolic process. A protein-protein interaction (PPI) analysis detected the top 10 hub genes (QSOX1, WFS1, EVA1A, FSTL3, CHRDL1, FABP4, PRDM16, PPARGC1A, PPARG, COL23A1). Finally, survival analysis, clinical correlation analysis, and protein abundance validation confirmed that 3 of the 10 hub genes were associated with survival prognosis of patients with THCA, and 8 of them were associated with the clinical stages of THCA. In summary, we identified hub genes and key modules that were closely related to THCA, and validated these genes by survival analysis, clinical correlation analysis, and Human Protein Atlas image analysis. Our results provide important information that will help to elucidate the pathogenesis of THCA and identify novel candidate prognostic biomarkers and potential therapeutic targets.
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Affiliation(s)
- Yangwang Pan
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Bejing, People's Republic of China
| | - Linjing Wu
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Bejing, People's Republic of China
| | - Shuai He
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Bejing, People's Republic of China
| | - Jun Wu
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Bejing, People's Republic of China
| | - Tong Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Bejing, People's Republic of China
| | - Hongrui Zang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Bejing, People's Republic of China
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Haidar MN, Islam MB, Chowdhury UN, Rahman MR, Huq F, Quinn JMW, Moni MA. Network-based computational approach to identify genetic links between cardiomyopathy and its risk factors. IET Syst Biol 2020; 14:75-84. [PMID: 32196466 PMCID: PMC8687405 DOI: 10.1049/iet-syb.2019.0074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/23/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Cardiomyopathy (CMP) is a group of myocardial diseases that progressively impair cardiac function. The mechanisms underlying CMP development are poorly understood, but lifestyle factors are clearly implicated as risk factors. This study aimed to identify molecular biomarkers involved in inflammatory CMP development and progression using a systems biology approach. The authors analysed microarray gene expression datasets from CMP and tissues affected by risk factors including smoking, ageing factors, high body fat, clinical depression status, insulin resistance, high dietary red meat intake, chronic alcohol consumption, obesity, high-calorie diet and high-fat diet. The authors identified differentially expressed genes (DEGs) from each dataset and compared those from CMP and risk factor datasets to identify common DEGs. Gene set enrichment analyses identified metabolic and signalling pathways, including MAPK, RAS signalling and cardiomyopathy pathways. Protein-protein interaction (PPI) network analysis identified protein subnetworks and ten hub proteins (CDK2, ATM, CDT1, NCOR2, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E and HIST1H4L). Five transcription factors (FOXC1, GATA2, FOXL1, YY1, CREB1) and five miRNAs were also identified in CMP. Thus the authors' approach reveals candidate biomarkers that may enhance understanding of mechanisms underlying CMP and their link to risk factors. Such biomarkers may also be useful to develop new therapeutics for CMP.
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Affiliation(s)
- Md Nasim Haidar
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj 6751, Bangladesh
| | - Fazlul Huq
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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Rana HK, Akhtar MR, Islam MB, Ahmed MB, Lió P, Huq F, Quinn JMW, Moni MA. Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression. Sci Rep 2020; 10:2795. [PMID: 32066756 PMCID: PMC7026442 DOI: 10.1038/s41598-020-57916-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/21/2019] [Indexed: 12/13/2022] Open
Abstract
Welding generates and releases fumes that are hazardous to human health. Welding fumes (WFs) are a complex mix of metallic oxides, fluorides and silicates that can cause or exacerbate health problems in exposed individuals. In particular, WF inhalation over an extended period carries an increased risk of cancer, but how WFs may influence cancer behaviour or growth is unclear. To address this issue we employed a quantitative analytical framework to identify the gene expression effects of WFs that may affect the subsequent behaviour of the cancers. We examined datasets of transcript analyses made using microarray studies of WF-exposed tissues and of cancers, including datasets from colorectal cancer (CC), prostate cancer (PC), lung cancer (LC) and gastric cancer (GC). We constructed gene-disease association networks, identified signaling and ontological pathways, clustered protein-protein interaction network using multilayer network topology, and analyzed survival function of the significant genes using Cox proportional hazards (Cox PH) model and product-limit (PL) estimator. We observed that WF exposure causes altered expression of many genes (36, 13, 25 and 17 respectively) whose expression are also altered in CC, PC, LC and GC. Gene-disease association networks, signaling and ontological pathways, protein-protein interaction network, and survival functions of the significant genes suggest ways that WFs may influence the progression of CC, PC, LC and GC. This quantitative analytical framework has identified potentially novel mechanisms by which tissue WF exposure may lead to gene expression changes in tissue gene expression that affect cancer behaviour and, thus, cancer progression, growth or establishment.
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Affiliation(s)
- Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Dhaka, Bangladesh
| | - Mst Rashida Akhtar
- Department of Computer Science and Engineering, Varendra University, Rajshahi, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Boshir Ahmed
- Bio-electronics Materials Laboratory, School of Materials Science and Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju, 500-712, Republic of Korea
| | - Pietro Lió
- Computer Laboratory, Department of Computer Science and Technology, University of Cambridge, 15 JJ Thomson Avenue, Cambridge, CB3 0FD, UK
| | - Fazlul Huq
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mohammad Ali Moni
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia. .,Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
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Hossain MA, Saiful Islam SM, Quinn JM, Huq F, Moni MA. Machine learning and bioinformatics models to identify gene expression patterns of ovarian cancer associated with disease progression and mortality. J Biomed Inform 2019; 100:103313. [DOI: 10.1016/j.jbi.2019.103313] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 09/20/2019] [Accepted: 10/13/2019] [Indexed: 02/07/2023]
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