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Prognostic biomarkers and molecular pathways mediating Helicobacter pylori-induced gastric cancer: a network-biology approach. 预后生物标志物和介导幽门螺杆菌诱导胃癌的分子途径:网络生物学方法。
Q2 Agricultural and Biological Sciences Pub Date : 2023-03-01 DOI: 10.5808/gi.22072
Farideh Kamarehei, Massoud Saidijam, Amir Taherkhani

Cancer of the stomach is the second most frequent cancer-related death worldwide. The survival rate of patients with gastric cancer (GC) remains fragile. There is a requirement to discover biomarkers for prognosis approaches. Helicobacter pylori in the stomach is closely associated with the progression of GC. We identified the genes associated with poor/favorable prognosis in H. pylori-induced GC. Multivariate statistical analysis was applied on the Gene Expression Omnibus (GEO) dataset GSE54397 to identify differentially expressed miRNAs (DEMs) in gastric tissues with H. pylori-induced cancer compared with the H. pylori-positive with non-cancerous tissue. A protein interaction map (PIM) was built and subjected to DEMs targets. The enriched pathways and biological processes within the PIM were identified based on substantial clusters. Thereafter, the most critical genes in the PIM were illustrated, and their prognostic impact in GC was investigated. Considering p-value less than 0.01 and |Log2 fold change| as >1, five microRNAs demonstrated significant changes among the two groups. Gene functional analysis revealed that the ubiquitination system, neddylation pathway, and ciliary process are primarily involved in H. pylori-induced GC. Survival analysis illustrated that the overexpression of DOCK4, GNAS, CTGF, TGF-b1, ESR1, SELE, TIMP3, SMARCE1, and TXNIP was associated with poor prognosis, while increased MRPS5 expression was related to a favorable prognosis in GC patients. DOCK4, GNAS, CTGF, TGF-b1, ESR1, SELE, TIMP3, SMARCE1, TXNIP, and MRPS5 may be considered prognostic biomarkers for H. pylori-induced GC. However, experimental validation is necessary in the future.

胃癌是世界上第二常见的癌症相关死亡。胃癌(GC)患者的生存率仍然很脆弱。有必要发现预后方法的生物标志物。胃内幽门螺杆菌与胃癌的进展密切相关。我们确定了与幽门螺杆菌诱导的GC预后不良/良好相关的基因。采用基因表达综合(GEO)数据集GSE54397进行多变量统计分析,以鉴定幽门螺杆菌诱导的胃癌组织与幽门螺杆菌阳性和非癌组织中差异表达的miRNAs (DEMs)。构建蛋白相互作用图谱(PIM),并将其置于dem靶标下。在PIM内的富集途径和生物过程是基于实质性集群确定的。随后,我们阐明了PIM中最关键的基因,并研究了它们对胃癌的预后影响。考虑p值< 0.01,Log2倍变化| >1,两组间有5个microrna发生显著变化。基因功能分析显示,在幽门螺杆菌诱导的GC中,泛素化系统、泛素化途径和纤毛过程主要参与。生存分析显示,DOCK4、GNAS、CTGF、TGF-b1、ESR1、SELE、TIMP3、SMARCE1、TXNIP过表达与预后不良相关,MRPS5表达升高与预后良好相关。DOCK4、GNAS、CTGF、TGF-b1、ESR1、SELE、TIMP3、SMARCE1、TXNIP和MRPS5可能被认为是幽门螺杆菌诱导的GC的预后生物标志物。然而,在未来,实验验证是必要的。
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引用次数: 0
Introduction of the Korea BioData Station (K-BDS) for sharing biological data. 引进共享生物数据的韩国生物数据站(K-BDS)。
Q2 Agricultural and Biological Sciences Pub Date : 2023-03-01 DOI: 10.5808/gi.22073
Byungwook Lee, Seungwoo Hwang, Pan-Gyu Kim, Gunwhan Ko, Kiwon Jang, Sangok Kim, Jong-Hwan Kim, Jongbum Jeon, Hyerin Kim, Jaeeun Jung, Byoung-Ha Yoon, Iksu Byeon, Insu Jang, Wangho Song, Jinhyuk Choi, Seon-Young Kim

A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates. To address these problems, in 2020, the Korean government officially announced a national strategy to collect and manage the biological data produced through national R&D fund allocations and provide the collected data to researchers. To this end, the Korea Bioinformation Center (KOBIC) developed a new biological data repository, the Korea BioData Station (K-BDS), for sharing data from individual researchers and research programs to create a data-driven biological study environment. The K-BDS is dedicated to providing free open access to a suite of featured data resources in support of worldwide activities in both academia and industry.

一波新技术浪潮为经济高效地生成高通量生物系统图谱创造了机会,预示着“数据驱动的科学”时代的到来。从生物研究中获得的大量数据也是一种丰富的资源,可以用于创新努力。然而,由于生物数据的复杂性及其以前所未有的指数速度产生,我们在大数据沉积、整合和转化方面面临着相当大的挑战。为了解决这些问题,韩国政府于2020年正式公布了收集和管理通过国家研发基金拨款产生的生物数据并向研究人员提供这些数据的国家战略。为此,韩国生物信息中心(KOBIC)开发了一个新的生物数据存储库——韩国生物数据站(K-BDS),用于共享个人研究人员和研究项目的数据,以创建数据驱动的生物研究环境。K-BDS致力于提供一套免费开放的特色数据资源,以支持学术界和工业界的全球活动。
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引用次数: 3
PyOncoPrint: a python package for plotting OncoPrints. pyoncopprint:用于绘制oncopprint的python包。
Q2 Agricultural and Biological Sciences Pub Date : 2023-03-01 DOI: 10.5808/gi.22079
Jeongbin Park, Nagarajan Paramasivam

OncoPrint, the plot to visualize an overview of genetic variants in sequencing data, has been widely used in the field of cancer genomics. However, still, there have been no Python libraries capable to generate OncoPrint yet, a big hassle to plot OncoPrints within Python-based genetic variants analysis pipelines. This paper introduces a new Python package PyOncoPrint, which can be easily used to plot OncoPrints in Python. The package is based on the existing widely used scientific plotting library Matplotlib, the resulting plots are easy to be adjusted for various needs.

oncopprint是一种在测序数据中可视化遗传变异概览的绘图,已广泛应用于癌症基因组学领域。然而,目前还没有能够生成oncopprint的Python库,在基于Python的遗传变异分析管道中绘制oncopprint是一个很大的麻烦。本文介绍了一个新的Python包pyoncopprint,它可以很容易地在Python中绘制oncopprint。该软件包基于现有广泛使用的科学绘图库Matplotlib,生成的绘图易于根据各种需求进行调整。
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引用次数: 0
Comprehensive investigation of the expression profiles of common long noncoding RNAs during microglial activation. 小胶质细胞活化过程中常见长链非编码rna表达谱的综合研究。
Q2 Agricultural and Biological Sciences Pub Date : 2023-03-01 DOI: 10.5808/gi.22061
Jung Ho Lee, Brian H Lee, Soyoung Jeong, Christine Suh-Yun Joh, Hyo Jeong Nam, Hyun Seung Choi, Henry Sserwadda, Ji Won Oh, Chung-Gyu Park, Seon-Pil Jin, Hyun Je Kim

Microglia, similar to peripheral macrophages, are the primary immune cells of the central nervous system (CNS). Microglia exist in the resting state in the healthy CNS, but can be activated and polarized into either M1 or M2 subtypes for immune defense and the maintenance of CNS homeostasis by multiple stimuli. Several long noncoding RNAs (lncRNAs) mediate human inflammatory diseases and neuropathologies by regulating their target genes. However, the function of common lncRNAs that contribute to microglial activation remains unclear. Thus, we used bioinformatic approaches to identify common lncRNAs involved in microglial activation in vitro. Our study identified several lncRNAs as common regulators of microglial activation. We identified 283 common mRNAs and 53 common lncRNAs during mouse M1 microglial activation processes, whereas 26 common mRNAs and five common lncRNAs were identified during mouse M2 microglial activation processes. A total of 648 common mRNAs and 274 common lncRNAs were identified during the activation of human M1 microglia. In addition, we identified 1,920 common co-expressed pairs in mouse M1 activation processes and 25 common co-expressed pairs in mouse M2 activation processes. Our study provides a comprehensive understanding of common lncRNA expression profiles in microglial activation processes in vitro. The list of common lncRNAs identified in this study provides novel evidence and clues regarding the molecular mechanisms underlying microglial activation.

与外周巨噬细胞类似,小胶质细胞是中枢神经系统(CNS)的初级免疫细胞。小胶质细胞在健康的中枢神经系统中处于静息状态,但在多种刺激下可被激活并极化为M1或M2亚型,用于免疫防御和维持中枢神经系统稳态。一些长链非编码rna (lncRNAs)通过调控其靶基因介导人类炎症性疾病和神经病理。然而,参与小胶质细胞激活的常见lncrna的功能尚不清楚。因此,我们使用生物信息学方法在体外鉴定参与小胶质细胞激活的常见lncrna。我们的研究确定了几种lncrna作为小胶质细胞激活的共同调节因子。我们在小鼠M1小胶质细胞激活过程中鉴定了283种常见mrna和53种常见lncrna,而在小鼠M2小胶质细胞激活过程中鉴定了26种常见mrna和5种常见lncrna。在人M1小胶质细胞的激活过程中,共鉴定出648种常见mrna和274种常见lncrna。此外,我们在小鼠M1激活过程中鉴定了1,920对共同表达对,在小鼠M2激活过程中鉴定了25对共同表达对。我们的研究提供了对体外小胶质细胞激活过程中常见lncRNA表达谱的全面了解。本研究中发现的常见lncrna列表为小胶质细胞激活的分子机制提供了新的证据和线索。
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引用次数: 0
Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family. 叉齿齿科6个新的线粒体全基因组的鉴定及该科系统发育关系的思考。
Q2 Agricultural and Biological Sciences Pub Date : 2023-03-01 DOI: 10.5808/gi.22041
Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegidio, Karine Frehner Kavalco

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

叉齿鱼科的鱼类,被称为吞鱼,是适应深海生活的物种。几项研究表明,这一家庭接近四足猴科和amarsiidae。然而,即使在系统基因组学研究中,该分支与其他白蛉类群的系统发育位置仍然不确定。由于已发表的有丝分裂基因组数量较少,我们的研究旨在从数据库库中组装6个新的Chiasmodontidae线粒体基因组,以扩大对该类群在低等形目中系统发育的讨论。正如预期的那样,在所分析的物种中,有丝分裂基因组的组成和组织是稳定的,尽管我们在Kali属物种的d -环中发现了重复序列,而在Chiasmodon, Dysalotus和Pseudoscopelus中没有发现。我们的系统发育纳入了来自几个伞形目科的51个有丝分裂基因组,包括9个交叉齿目,恢复了在以前的研究中建立的家族间关系,包括一个包含交叉齿科、amarsiidae和Tetragonuridae的分支。然而,大型进化枝之间的系统发育关系仍然不清楚,不同的系统发育研究之间存在分歧。我们认为,这种不一致性不仅是由于数据的偏差和局限性,而且主要是由于白垩纪-古近纪灭绝事件后的复杂生物事件。
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引用次数: 0
Generation and analysis of whole-genome sequencing data in human mammary epithelial cells. 人乳腺上皮细胞全基因组测序数据的生成与分析。
Q2 Agricultural and Biological Sciences Pub Date : 2023-03-01 DOI: 10.5808/gi.22044
Jong-Lyul Park, Jae-Yoon Kim, Seon-Young Kim, Yong Sun Lee

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during the progression of breast carcinogenesis. Here, we report a dataset of whole genomes from the human mammary epithelial cell system derived from a reduction mammoplasty specimen. This system comprises pre-stasis 184D cells, considered normal, and seven cell lines along cancer progression series that are immortalized or additionally acquired anchorage-independent growth. Our analysis of the whole-genome sequencing (WGS) data indicates that those seven cancer progression series cells have somatic mutations whose number ranges from 8,393 to 39,564 (with an average of 30,591) compared to 184D cells. These WGS data and our mutation analysis will provide helpful information to identify driver mutations and elucidate molecular mechanisms for breast carcinogenesis.

乳腺癌是世界上最常见的癌症,晚期乳腺癌转移是无法治愈的,主要是目前可用的治疗方法。因此,了解乳腺癌发生过程中的分子特征是至关重要的。在这里,我们报告了来自缩小乳房成形术标本的人类乳腺上皮细胞系统的全基因组数据集。该系统包括停滞前的184D细胞,被认为是正常的,以及沿着癌症进展系列的7个细胞系,这些细胞系是永生化的或额外获得了不依赖于锚定的生长。我们对全基因组测序(WGS)数据的分析表明,与184D细胞相比,这7个癌症进展系列细胞的体细胞突变数量在8,393到39,564之间(平均为30,591)。这些WGS数据和我们的突变分析将为识别驱动突变和阐明乳腺癌发生的分子机制提供有用的信息。
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引用次数: 0
A Python-based educational software tool for visualizing bioinformatics alignment algorithms. 一个基于python的教育软件工具,用于可视化生物信息学对齐算法。
Q2 Agricultural and Biological Sciences Pub Date : 2023-03-01 DOI: 10.5808/gi.22055
Elis Khatizah, Hee-Jo Nam, Hyun-Seok Park

Bioinformatics education can be defined as the teaching and learning of how to use software tools, along with mathematical and statistical analysis, to solve biological problems. Although many resources are available, most students still struggle to understand even the simplest sequence alignment algorithms. Applying visualizations to these topics benefits both lecturers and students. Unfortunately, educational software for visualizing step-bystep processes in the user experience of sequence alignment algorithms is rare. In this article, an educational visualization tool for biological sequence alignment is presented, and the source code is released in order to encourage the collaborative power of open-source software, with the expectation of further contributions from the community in the future. Two different modules are integrated to enable a student to investigate the characteristics of alignment algorithms.

生物信息学教育可以定义为教授和学习如何使用软件工具以及数学和统计分析来解决生物学问题。尽管有很多可用的资源,但大多数学生仍然很难理解最简单的序列比对算法。将可视化应用于这些主题对讲师和学生都有好处。不幸的是,教育软件可视化一步一步的过程,在用户体验的序列比对算法是罕见的。在本文中,介绍了一个用于生物序列比对的教育可视化工具,并发布了源代码,以鼓励开源软件的协作能力,并期望社区在未来做出进一步的贡献。两个不同的模块集成,使学生能够研究对齐算法的特点。
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引用次数: 0
Beta-Meta: a meta-analysis application considering heterogeneity among genome-wide association studies. meta:一项考虑全基因组关联研究异质性的meta分析应用。
Q2 Agricultural and Biological Sciences Pub Date : 2022-12-01 DOI: 10.5808/gi.22046
Gyungbu Kim, Yoonsuk Lee, Jeong Ho Park, Dongmin Kim, Wonseok Lee

Many packages for a meta-analysis of genome-wide association studies (GWAS) have beendeveloped to discover genetic variants. Although variations across studies must be considered, there are not many currently-accessible packages that estimate between-study heterogeneity. Thus, we propose a python based application called Beta-Meta which can easilyprocess a meta-analysis by automatically selecting between a fixed effects and a randomeffects model based on heterogeneity. Beta-Meta implements flexible input data manipulation to allow multiple meta-analyses of different genotype-phenotype associations in asingle process. It provides a step-by-step meta-analysis of GWAS for each association inthe following order: heterogeneity test, two different calculations of an effect size and ap-value based on heterogeneity, and the Benjamini-Hochberg p-value adjustment. Thesemethods enable users to validate the results of individual studies with greater statisticalpower and better estimation precision. We elaborate on these and illustrate them with examples from several studies of infertility-related disorders.

许多包的荟萃分析的全基因组关联研究(GWAS)已经开发发现遗传变异。虽然必须考虑研究之间的差异,但目前可获得的评估研究之间异质性的软件包并不多。因此,我们提出了一个基于python的应用程序,称为Beta-Meta,它可以通过自动选择基于异质性的固定效应和随机效应模型来轻松地处理元分析。Beta-Meta实现了灵活的输入数据操作,允许在一个过程中对不同的基因型-表型关联进行多重荟萃分析。它按以下顺序提供了对每个关联的GWAS的逐步元分析:异质性检验,基于异质性的效应大小和ap值的两种不同计算,以及Benjamini-Hochberg p值调整。这些方法使用户能够以更大的统计能力和更好的估计精度验证单个研究的结果。我们详细说明这些,并举例说明他们从几个研究不孕症相关的障碍。
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引用次数: 0
In silico detection and characterization of novel virulence proteins of the emerging poultry pathogen Gallibacterium anatis. 新兴家禽病原体鸭芽孢杆菌新型毒力蛋白的计算机检测与鉴定。
Q2 Agricultural and Biological Sciences Pub Date : 2022-12-01 DOI: 10.5808/gi.22006
L G T G Rajapaksha, C W R Gunasekara, P S D Alwis

The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.

病原体猪链球菌给世界各地的商业家禽养殖场造成了严重的经济损失。然而,尽管它很重要,但其假设蛋白(hp)的功能却没有得到很好的表征。本研究利用多种生物信息学工具分析了从鸭芽孢杆菌(Gallibacterium anatis, NCTC11413)中获得的hp的功能和结构。最初,使用VICMpred工具预测hp的所有功能,然后使用Expasy的ProtParam服务器分析鉴定的毒力蛋白的物理化学性质。进一步分析可作为潜在药物靶点的毒力蛋白(WP_013745346.1)二级结构,利用Swiss-Model和Phyre2服务器进行同源性建模和三维(3D)结构测定。采用ERRAT、Verify3D和PROCHECK程序对三维模型进行质量评估和验证。使用ProFunc、STRING、KEGG服务器和MEGA软件进行功能和系统发育分析。生物信息学分析显示,201个hp与细胞过程(n = 119)、代谢(n = 61)、毒力(n = 11)和信息/存储分子(n = 10)有关。在毒力蛋白中,检测到3个作为药物靶点,6个作为疫苗靶点。表征的毒力蛋白WP_013745346.1在目前的病原体中被证明是稳定的,是一个药物靶点,也是一个与柠檬酸循环相关的酶。该酶还被发现促进其他代谢途径,次生代谢物的生物合成和氨基酸的生物合成。
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引用次数: 1
Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome. 泰国Brugada综合征患者全基因组测序数据中整合病毒基因的宏基因组分析
Q2 Agricultural and Biological Sciences Pub Date : 2022-12-01 DOI: 10.5808/gi.22047
Suwalak Chitcharoen, Chureerat Phokaew, John Mauleekoonphairoj, Apichai Khongphatthanayothin, Boosamas Sutjaporn, Pharawee Wandee, Yong Poovorawan, Koonlawee Nademanee, Sunchai Payungporn

Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of patients with BS still have unclear disease etiology. Here, we performeda new viral metagenome analysis pipeline called VIRIN and validated it with whole genome sequencing (WGS) data of HeLa cell lines and hepatocellular carcinoma. Then the VIRIN pipelinewas applied to identify viral integration positions from unmapped WGS data of Thai males, including 100 BS patients (case) and 100 controls. Even though the sample preparation had noviral enrichment step, we can identify several virus genes from our analysis pipeline. The predominance of human endogenous retrovirus K (HERV-K) viruses was found in both cases andcontrols by blastn and blastx analysis. This study is the first report on the full-length HERV-Kassembled genomes in the Thai population. Furthermore, the HERV-K integration breakpointpositions were validated and compared between the case and control datasets. Interestingly,Brugada cases contained HERV-K integration breakpoints at promoters five times more oftenthan controls. Overall, the highlight of this study is the BS-specific HERV-K breakpoint positionsthat were found at the gene coding region "NBPF11" (n = 9), "NBPF12" (n = 8) and longnon-coding RNA (lncRNA) "PCAT14" (n = 4) region. The genes and the lncRNA have been reported to be associated with congenital heart and arterial diseases. These findings provide another aspect of the BS etiology associated with viral genome integrations within the humangenome.

Brugada综合征(BS)是一种常染色体显性遗传的与猝死相关的年轻成人心律失常疾病。泰国是全球BS患病率最高的国家,超过60%的BS患者病因不明。在这里,我们建立了一个新的病毒宏基因组分析管道,称为VIRIN,并用HeLa细胞系和肝癌的全基因组测序(WGS)数据验证了它。然后应用VIRIN管道从未定位的泰国男性WGS数据中识别病毒整合位置,包括100例BS患者(病例)和100例对照。尽管样品制备中没有病毒富集步骤,但我们可以从我们的分析管道中识别出几种病毒基因。通过胚细胞和母细胞分析发现,人内源性逆转录病毒K (HERV-K)病毒在病例和对照组中均占优势。本研究是泰国人群中首次报道的herv - k组装全长基因组。此外,在病例和对照数据集之间验证并比较了HERV-K积分断点位置。有趣的是,Brugada病例在启动子处包含HERV-K整合断点的频率是对照组的5倍。总的来说,本研究的亮点是在基因编码区“NBPF11”(n = 9)、“NBPF12”(n = 8)和长链非编码RNA (lncRNA)上发现了bs特异性HERV-K断点位置。“PCAT14”(n = 4)区域。据报道,这些基因和lncRNA与先天性心脏和动脉疾病有关。这些发现提供了与人类基因组内病毒基因组整合相关的BS病因学的另一个方面。
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引用次数: 1
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