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薛 继, 刘 静, 耿 淼, 岳 敬, 贺 浩, 范 皎. [Identification of potential hub genes of Alzheimer's disease by weighted gene co-expression network analysis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1752-1762. [PMID: 35012905 PMCID: PMC8752417 DOI: 10.12122/j.issn.1673-4254.2021.12.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To investigate the differential expression gene modules and hub genes associated with Alzheimer's disease (AD) by weighted gene co-expression network analysis (WGCNA) and annotate the biological functions of these modules. METHODS We downloaded transcriptome sequencing data from the GEO database, and according to the correlation of the genes, a gene co-expression network was constructed with the parameter setting of β=8 and a correlation coefficient threshold of 0.85. Pearson correlation test was used to calculate the correlation between the module genes and clinical traits to screen the gene modules significantly associated with AD and identify the hub genes according to the connectivity within modules. GO functional enrichment analysis and KEGG pathway analysis were used to annotate the functions of the modules. A cell model of AD was established in SH-SY5Y cells by Aβ1-42 treatment, and the mRNA expression levels of the hub genes were compared between the Aβ1-42-treated cells and the control cells. RESULTS Ten gene co-expression modules were constructed based on the correlations of gene expression, in which the brown (r=0.66, P < 0.001) and turquoise modules (r=-0.68, P < 0.001) were significantly correlated with the AD group. Forty-eight genes were identified as the hub genes in the co-expression network. Function annotation revealed that the genes in both modules were mainly enriched in DNA damage and repair pathways and metabolism-related pathways. Differential expression analysis of the genes revealed that the genes DNASE1, TEKT2 and MTSS1L were highly expressed while ACP2, LANCL2 and GMPR2 were lowly expressed in AD group. The results of cell experiment confirmed the up-regulation of DNASE1, TEKT2 and MTSS1L genes and the down-regulation of ACP2, LANCL2, and GMPR2 in Aβ1-42-treated SH-SY5Y cells (P < 0.01). CONCLUSION The brown and turquoise modules are closely correlated with AD. The hub genes including MTSS1L, GMPR2, ACP2, ACTG1 and LANCL2 selected from the modules may participate in AD pathogenesis by regulating DNA damage and repair.
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Affiliation(s)
- 继国 薛
- 中国人民解放军军事科学院军事医学研究院辐射医学研究所,北京 100850Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - 静 刘
- 中国人民解放军总医院第二医学中心老年医学研究所,国家老年疾病临床医学研究中心,北京 100853Institute of Geriatrics, Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - 淼 耿
- 中国人民解放军总医院第二医学中心老年医学研究所,国家老年疾病临床医学研究中心,北京 100853Institute of Geriatrics, Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - 敬伟 岳
- 中国人民解放军军事科学院军事医学研究院辐射医学研究所,北京 100850Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - 浩宸 贺
- 中国人民解放军军事科学院军事医学研究院辐射医学研究所,北京 100850Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - 皎 范
- 中国人民解放军总医院第二医学中心老年医学研究所,国家老年疾病临床医学研究中心,北京 100853Institute of Geriatrics, Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
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Shaw GTW, Shih ESC, Chen CH, Hwang MJ. Preservation of ranking order in the expression of human Housekeeping genes. PLoS One 2011; 6:e29314. [PMID: 22216246 PMCID: PMC3245260 DOI: 10.1371/journal.pone.0029314] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 11/24/2011] [Indexed: 01/26/2023] Open
Abstract
Housekeeping (HK) genes fulfill the basic needs for a cell to survive and function properly. Their ubiquitous expression, originally thought to be constant, can vary from tissue to tissue, but this variation remains largely uncharacterized and it could not be explained by previously identified properties of HK genes such as short gene length and high GC content. By analyzing microarray expression data for human genes, we uncovered a previously unnoted characteristic of HK gene expression, namely that the ranking order of their expression levels tends to be preserved from one tissue to another. Further analysis by tensor product decomposition and pathway stratification identified three main factors of the observed ranking preservation, namely that, compared to those of non-HK (NHK) genes, the expression levels of HK genes show a greater degree of dispersion (less overlap), stableness (a smaller variation in expression between tissues), and correlation of expression. Our results shed light on regulatory mechanisms of HK gene expression that are probably different for different HK genes or pathways, but are consistent and coordinated in different tissues.
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Affiliation(s)
- Grace T. W. Shaw
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Edward S. C. Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chun-Houh Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Ming-Jing Hwang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Hong BH, Oh SJ, Ju J, Hong BJ, Jang DS, Yun YS, Park JW, Choi KY. Oligonucleotide microarrays with high discriminating power for the detection of single nucleotide variations in the p53 gene. Mol Cells 2010; 30:575-9. [PMID: 21120630 DOI: 10.1007/s10059-010-0144-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 07/14/2010] [Accepted: 08/30/2010] [Indexed: 10/18/2022] Open
Affiliation(s)
- Bee Hak Hong
- Division of Molecular and Life Sciences and POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 790-784, Korea
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Plant N. Expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs): What large-scale sequencing projects can tell us about ADME. Xenobiotica 2009; 36:860-76. [PMID: 17118912 DOI: 10.1080/00498250600861603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
To date over 800 complete genomes have been sequenced, with many more partially complete. Coupled with the large amount of mRNA transcript sequence data being produced from expression studies, there is now a daunting amount of information available to the research scientist. This review examines how this information may be best used, focusing on examples from sequences encoding absorption, distribution, metabolism and excretion (ADME)-related proteins in particular. Through the use of phylogenetic, splice variant and single nucleotide polymorphism (SNP) analysis, the review examines not only how insights into species-specific responses to drug exposure may be gained, but also how best to utilize this information to predict both individual human responses and the impact of population variance in response.
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Affiliation(s)
- N Plant
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford, UK.
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Risques RA, Rondeau G, Judex M, McClelland M, Welsh J. Assessment of gene expression in many samples using vertical arrays. Nucleic Acids Res 2008; 36:e60. [PMID: 18474526 PMCID: PMC2425485 DOI: 10.1093/nar/gkn263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Microarrays and high-throughput sequencing methods can be used to measure the expression of thousands of genes in a biological sample in a few days, whereas PCR-based methods can be used to measure the expression of a few genes in thousands of samples in about the same amount of time. These methods become more costly as the number of biological samples increases or as the number of genes of interest increases, respectively, and these factors constrain experimental design. To address these issues, we introduced ‘vertical arrays’ in which RNA from each biological sample is converted into multiple, overlapping cDNA subsets and spotted on glass slides. These vertical arrays can be queried with single gene probes to assess the expression behavior in thousands of biological samples in a single hybridization reaction. The spotted subsets are less complex than the original RNA from which they derive, which improves signal-to-noise ratios. Here, we demonstrate the quantitative capabilities of vertical arrays, including the sensitivity and accuracy of the method and the number of subsets needed to achieve this accuracy for most expressed genes.
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Affiliation(s)
- Rosa Ana Risques
- Sidney Kimmel Cancer Center, 10905 Road to the Cure, San Diego, CA 92121, USA
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Oh SJ, Ju J, Kim BC, Ko E, Hong BJ, Park JG, Park JW, Choi KY. DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene. Nucleic Acids Res 2005; 33:e90. [PMID: 15939931 PMCID: PMC1143581 DOI: 10.1093/nar/gni087] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2005] [Revised: 05/16/2005] [Accepted: 05/16/2005] [Indexed: 12/13/2022] Open
Abstract
Selectivity and sensitivity in the detection of single nucleotide polymorphisms (SNPs) are among most important attributes to determine the performance of DNA microarrays. We previously reported the generation of a novel mesospaced surface prepared by applying dendron molecules on the solid surface. DNA microarrays that were fabricated on the dendron-modified surface exhibited outstanding performance for the detection of single nucleotide variation in the synthetic oligonucleotide DNA. DNA microarrays on the dendron-modified surface were subjected to the detection of single nucleotide variations in the exons 5-8 of the p53 gene in genomic DNAs from cancer cell lines. DNA microarrays on the dendron-modified surface clearly discriminated single nucleotide variations in hotspot codons with high selectivity and sensitivity. The ratio between the fluorescence intensity of perfectly matched duplexes and that of single nucleotide mismatched duplexes was >5-100 without sacrificing signal intensity. Our results showed that the outstanding performance of DNA microarrays fabricated on the dendron-modified surface is strongly related to novel properties of the dendron molecule, which has the conical structure allowing mesospacing between the capture probes. Our microarrays on the dendron-modified surface can reduce the steric hindrance not only between the solid surface and target DNA, but also among immobilized capture probes enabling the hybridization process on the surface to be very effective. Our DNA microarrays on the dendron-modified surface could be applied to various analyses that require accurate detection of SNPs.
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Affiliation(s)
- Soon Jin Oh
- Division of Molecular and Life Sciences, Pohang University of Science and TechnologyPohang 790-784, Korea
- Research Institute and Hospital, National Cancer CenterGoyang, 411-764, Korea
| | - Jimin Ju
- Division of Molecular and Life Sciences, Pohang University of Science and TechnologyPohang 790-784, Korea
- Research Institute and Hospital, National Cancer CenterGoyang, 411-764, Korea
| | - Byung Chul Kim
- Division of Molecular and Life Sciences, Pohang University of Science and TechnologyPohang 790-784, Korea
- Research Institute and Hospital, National Cancer CenterGoyang, 411-764, Korea
| | - Eunsil Ko
- Division of Molecular and Life Sciences, Pohang University of Science and TechnologyPohang 790-784, Korea
- Research Institute and Hospital, National Cancer CenterGoyang, 411-764, Korea
| | - Bong Jin Hong
- Division of Molecular and Life Sciences, Pohang University of Science and TechnologyPohang 790-784, Korea
- Research Institute and Hospital, National Cancer CenterGoyang, 411-764, Korea
| | - Jae-Gahb Park
- Research Institute and Hospital, National Cancer CenterGoyang, 411-764, Korea
| | - Joon Won Park
- Division of Molecular and Life Sciences, Pohang University of Science and TechnologyPohang 790-784, Korea
- Research Institute and Hospital, National Cancer CenterGoyang, 411-764, Korea
| | - Kwan Yong Choi
- To whom correspondence should be addressed. Tel: +82 54 279 2295; Fax: +82 54 279 8290;
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Yang HL, Jiang HJ, Fang WY, Xu YY, Li K, Zhang J, Liao DF, He FC. High fidelity PCR with an off/on switch mediated by proofreading polymerases combining with phosphorothioate-modified primer. Biochem Biophys Res Commun 2005; 328:265-72. [PMID: 15670779 DOI: 10.1016/j.bbrc.2004.12.159] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Indexed: 11/22/2022]
Abstract
In the initial report, introducing a single phosphorothioate modification at the very 3' terminus of the oligodeoxynucleotide primer has been shown to effectively protect the oligodeoxynucleotide degradation due to the 3' exonuclease activity. In this study, we reported a novel finding that phosphorothioate modification at the 3' end of primers could not only effectively prevent the primer from degradation, but could also mediate an off-switch extension by Pfu polymerase when primers also carry single or multiple mismatched bases located in the first eight bases of the 3' terminus. This suggests that the combination of 3' phosphorothioate-modified primers with exo+ polymerases such as Pfu constituted an on/off switch, which allows perfectly matched primers to be extended but not mismatched primers. Furthermore, we found that polymerases with different fidelities showed different efficiencies in turning off mismatched-primer mediated extension. So we described here a SYBR green-based real-time quantitative PCR assay for the detection of abundance level of gene expression that did not require fluorescently labeled gene-specific probes or complicated primer combinations. The emergence of real-time quantitative RT-PCR technology is thus suited for a diverse application with a need for high-throughput methods to detect and quantify different gene expressions by way of simplicity, versatility, and accuracy, and thus could complement global microarray-based expression profiling strategies.
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Affiliation(s)
- Hui-Ling Yang
- SNP Institute, Institute of Pharmacy and Pharmacology, Nanhua University, Hengyang 421001, Hunan, China
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