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Hu Y, Zhou J. Identification of key genes and functional enrichment analysis of liver fibrosis in nonalcoholic fatty liver disease through weighted gene co-expression network analysis. Genomics Inform 2023; 21:e45. [PMID: 38224712 PMCID: PMC10788356 DOI: 10.5808/gi.23051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common type of chronic liver disease, with severity levels ranging from nonalcoholic fatty liver to nonalcoholic steatohepatitis (NASH). The extent of liver fibrosis indicates the severity of NASH and the risk of liver cancer. However, the mechanism underlying NASH development, which is important for early screening and intervention, remains unclear. Weighted gene co-expression network analysis (WGCNA) is a useful method for identifying hub genes and screening specific targets for diseases. In this study, we utilized an mRNA dataset of the liver tissues of patients with NASH and conducted WGCNA for various stages of liver fibrosis. Subsequently, we employed two additional mRNA datasets for validation purposes. Gene set enrichment analysis (GSEA) was conducted to analyze gene function enrichment. Through WGCNA and subsequent analyses, complemented by validation using two additional datasets, we identified five genes (BICC1, C7, EFEMP1, LUM, and STMN2) as hub genes. GSEA analysis indicated that gene sets associated with liver metabolism and cholesterol homeostasis were uniformly downregulated. BICC1, C7, EFEMP1, LUM, and STMN2 were identified as hub genes of NASH, and were all related to liver metabolism, NAFLD, NASH, and related diseases. These hub genes might serve as potential targets for the early screening and treatment of NASH.
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Affiliation(s)
- Yue Hu
- Shenzhen InnoStar Institute of Biomedical Safety Evaluation and Research Co., Ltd., Shenzhen,518000, China
| | - Jun Zhou
- Shenzhen InnoStar Institute of Biomedical Safety Evaluation and Research Co., Ltd., Shenzhen,518000, China
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Liu W, Pan J, Xu Y, Wang M, Jia H, Zhang K, Chen X, Li X, Liao X. Fast and Accurate Motion Correction for Two-Photon Ca 2+ Imaging in Behaving Mice. Front Neuroinform 2022; 16:851188. [PMID: 35559212 PMCID: PMC9088923 DOI: 10.3389/fninf.2022.851188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Two-photon Ca2+ imaging is a widely used technique for investigating brain functions across multiple spatial scales. However, the recording of neuronal activities is affected by movement of the brain during tasks in which the animal is behaving normally. Although post-hoc image registration is the commonly used approach, the recent developments of online neuroscience experiments require real-time image processing with efficient motion correction performance, posing new challenges in neuroinformatics. We propose a fast and accurate image density feature-based motion correction method to address the problem of imaging animal during behaviors. This method is implemented by first robustly estimating and clustering the density features from two-photon images. Then, it takes advantage of the temporal correlation in imaging data to update features of consecutive imaging frames with efficient calculations. Thus, motion artifacts can be quickly and accurately corrected by matching the features and obtaining the transformation parameters for the raw images. Based on this efficient motion correction strategy, our algorithm yields promising computational efficiency on imaging datasets with scales ranging from dendritic spines to neuronal populations. Furthermore, we show that the proposed motion correction method outperforms other methods by evaluating not only computational speed but also the quality of the correction performance. Specifically, we provide a powerful tool to perform motion correction for two-photon Ca2+ imaging data, which may facilitate online imaging experiments in the future.
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Affiliation(s)
- Weiyi Liu
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Junxia Pan
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Yuanxu Xu
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Meng Wang
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Hongbo Jia
- Advanced Institute for Brain and Intelligence, Guangxi University, Nanning, China
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Kuan Zhang
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Xiaowei Chen
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Xingyi Li
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Xiang Liao
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
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Peng L, Ma W, Xie Q, Chen B. Identification and validation of hub genes for diabetic retinopathy. PeerJ 2021; 9:e12126. [PMID: 34603851 PMCID: PMC8445088 DOI: 10.7717/peerj.12126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
Background Diabetic retinopathy (DR) is characterized by a gradually progressive alteration in the retinal microvasculature that leads to middle-aged adult acquired persistent blindness. Limited research has been conducted on DR pathogenesis at the gene level. Thus, we aimed to reveal novel key genes that might be associated with DR formation via a bioinformatics analysis. Methods The GSE53257 dataset from the Gene Expression Omnibus was downloaded for gene co-expression analysis. We identified significant gene modules via the Weighted Gene Co-expression Network Analysis, which was conducted by the Protein-Protein Interaction (PPI) Network via Cytoscape and from this we screened for key genes and gene sets for particular functional and pathway-specific enrichments. The hub gene expression was verified by real-time PCR in DR rats modeling and an external database. Results Two significant gene modules were identified. Significant key genes were predominantly associated with mitochondrial function, fatty acid oxidation and oxidative stress. Among all key genes analyzed, six up-regulated genes (i.e., SLC25A33, NDUFS1, MRPS23, CYB5R1, MECR, and MRPL15) were highly and significantly relevant in the context of DR formation. The PCR results showed that SLC25A33 and NDUFS1 expression were increased in DR rats modeling group. Conclusion Gene co-expression network analysis highlights the importance of mitochondria and oxidative stress in the pathophysiology of DR. DR co-expressing gene module was constructed and key genes were identified, and both SLC25A33 and NDUFS1 may serve as potential biomarker and therapeutic target for DR.
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Affiliation(s)
- Li Peng
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.,Department of Ophthalmology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
| | - Wei Ma
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qing Xie
- Department of Ophthalmology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
| | - Baihua Chen
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Alexiou A, Chatzichronis S, Perveen A, Hafeez A, Ashraf GM. Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions. Curr Top Med Chem 2019; 19:413-425. [PMID: 30854971 DOI: 10.2174/1568026619666190311125256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/15/2018] [Accepted: 12/26/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Latest studies reveal the importance of Protein-Protein interactions on physiologic functions and biological structures. Several stochastic and algorithmic methods have been published until now, for the modeling of the complex nature of the biological systems. OBJECTIVE Biological Networks computational modeling is still a challenging task. The formulation of the complex cellular interactions is a research field of great interest. In this review paper, several computational methods for the modeling of GRN and PPI are presented analytically. METHODS Several well-known GRN and PPI models are presented and discussed in this review study such as: Graphs representation, Boolean Networks, Generalized Logical Networks, Bayesian Networks, Relevance Networks, Graphical Gaussian models, Weight Matrices, Reverse Engineering Approach, Evolutionary Algorithms, Forward Modeling Approach, Deterministic models, Static models, Hybrid models, Stochastic models, Petri Nets, BioAmbients calculus and Differential Equations. RESULTS GRN and PPI methods have been already applied in various clinical processes with potential positive results, establishing promising diagnostic tools. CONCLUSION In literature many stochastic algorithms are focused in the simulation, analysis and visualization of the various biological networks and their dynamics interactions, which are referred and described in depth in this review paper.
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Affiliation(s)
| | | | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Ghulam Md. Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Zhu B, Wang Y, Zhou X, Cao C, Zong Y, Zhao X, Sha Z, Zhao X, Han S. A Controlled Study of the Feasibility and Efficacy of a Cloud-Based Interactive Management Program Between Patients with Psoriasis and Physicians. Med Sci Monit 2019; 25:970-976. [PMID: 30713334 PMCID: PMC6371740 DOI: 10.12659/msm.913304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Dermatology patients continue to receive improved treatment, but for patients with psoriasis, there have been few studies on ways to improve patient management by improving communication with patients and their dermatologists. This study aimed to investigate the feasibility and efficacy of cloud-based interactive patient and physician management of psoriasis. MATERIAL AND METHODS The cloud-based platform was created by professional software engineers to educate and manage patients with psoriasis in a single hospital, where patients and research staff had a network platform for sharing data. A total of 79 patients with psoriasis were included in this study and were randomly divided into the control group (n=39) and the intervention group (n=40). Patients in the control group were given a psoriasis nursing manual and underwent regular follow-up. Patients in the intervention group were managed using the cloud platform, with the same management as the control group. The Psoriasis Area Severity Index (PASI), the Self-Rating Anxiety Scale (SAS), the Dermatology Life Quality Index (DLQI), and the Symptom Checklist-90-Revised (SCL-90-R) were used. RESULTS Cloud-based interactive patient and physician management resulted in clinical improvement, and reduced the degree of anxiety in patients with psoriasis and improved their physical and mental health. Patients in the intervention group had an improved understanding of psoriasis treatment, resulting in an improved relationship with the medical staff and improved treatment compliance. CONCLUSIONS Cloud-based interactive patient and physician management improved the mental health and quality of life for patients with psoriasis and allowed patients to manage their disease more effectively.
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Affiliation(s)
- Beibei Zhu
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Yanyan Wang
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Xuan Zhou
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Chunyan Cao
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Yan Zong
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Xiaodan Zhao
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Zuohong Sha
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Xiaoyun Zhao
- Department of Nursing, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, P.R. China
| | - Shanhang Han
- Department of Rheumatology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine (TCM), Nanjing, Jiangsu, P.R. China
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