Genomics and Informatics最新文献_第3页

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。

Genomics and Informatics Pub Date : 2023-03-01 DOI: 10.5808/gi.22072

Farideh Kamarehei, Massoud Saidijam, Amir Taherkhani

{"title":"Prognostic biomarkers and molecular pathways mediating Helicobacter pylori-induced gastric cancer: a network-biology approach.","authors":"Farideh Kamarehei, Massoud Saidijam, Amir Taherkhani","doi":"10.5808/gi.22072","DOIUrl":"https://doi.org/10.5808/gi.22072","url":null,"abstract":"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.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 1","pages":"e8"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9282403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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)。

Genomics and Informatics 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

{"title":"Introduction of the Korea BioData Station (K-BDS) for sharing biological data.","authors":"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","doi":"10.5808/gi.22073","DOIUrl":"https://doi.org/10.5808/gi.22073","url":null,"abstract":"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.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 1","pages":"e12"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9288426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

PyOncoPrint: a python package for plotting OncoPrints. pyoncopprint:用于绘制oncopprint的python包。

Genomics and Informatics Pub Date : 2023-03-01 DOI: 10.5808/gi.22079

Jeongbin Park, Nagarajan Paramasivam

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。

Genomics and Informatics 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

{"title":"Comprehensive investigation of the expression profiles of common long noncoding RNAs during microglial activation.","authors":"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","doi":"10.5808/gi.22061","DOIUrl":"https://doi.org/10.5808/gi.22061","url":null,"abstract":"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.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 1","pages":"e2"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10592798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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。

Genomics and Informatics Pub Date : 2023-03-01 DOI: 10.5808/gi.22041

Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegidio, Karine Frehner Kavalco

{"title":"Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family.","authors":"Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegidio, Karine Frehner Kavalco","doi":"10.5808/gi.22041","DOIUrl":"https://doi.org/10.5808/gi.22041","url":null,"abstract":"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.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 1","pages":"e10"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9282399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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。

Genomics and Informatics Pub Date : 2023-03-01 DOI: 10.5808/gi.22044

Jong-Lyul Park, Jae-Yoon Kim, Seon-Young Kim, Yong Sun Lee

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。

Genomics and Informatics Pub Date : 2023-03-01 DOI: 10.5808/gi.22055

Elis Khatizah, Hee-Jo Nam, Hyun-Seok Park

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。

Genomics and Informatics Pub Date : 2022-12-01 DOI: 10.5808/gi.22046

Gyungbu Kim, Yoonsuk Lee, Jeong Ho Park, Dongmin Kim, Wonseok Lee

{"title":"Beta-Meta: a meta-analysis application considering heterogeneity among genome-wide association studies.","authors":"Gyungbu Kim, Yoonsuk Lee, Jeong Ho Park, Dongmin Kim, Wonseok Lee","doi":"10.5808/gi.22046","DOIUrl":"https://doi.org/10.5808/gi.22046","url":null,"abstract":"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.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e49"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9156895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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。

Genomics and Informatics Pub Date : 2022-12-01 DOI: 10.5808/gi.22006

L G T G Rajapaksha, C W R Gunasekara, P S D Alwis

{"title":"In silico detection and characterization of novel virulence proteins of the emerging poultry pathogen Gallibacterium anatis.","authors":"L G T G Rajapaksha, C W R Gunasekara, P S D Alwis","doi":"10.5808/gi.22006","DOIUrl":"https://doi.org/10.5808/gi.22006","url":null,"abstract":"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.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e41"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10582627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Genomics and Informatics 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

{"title":"Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome.","authors":"Suwalak Chitcharoen, Chureerat Phokaew, John Mauleekoonphairoj, Apichai Khongphatthanayothin, Boosamas Sutjaporn, Pharawee Wandee, Yong Poovorawan, Koonlawee Nademanee, Sunchai Payungporn","doi":"10.5808/gi.22047","DOIUrl":"https://doi.org/10.5808/gi.22047","url":null,"abstract":"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.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e44"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10591857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1