Evren Atak , Dilara Karaoğlu , Seda Serttürk , Duygu Koyuncu Irmak , Aslı Yenenler-Kutlu
{"title":"通过比较分析了解基因在心肌病不同通路中的功能作用","authors":"Evren Atak , Dilara Karaoğlu , Seda Serttürk , Duygu Koyuncu Irmak , Aslı Yenenler-Kutlu","doi":"10.1016/j.mgene.2021.100975","DOIUrl":null,"url":null,"abstract":"<div><p>Personalized medicine is one of the popular approaches in biological sciences. Due to the great attention in personalized medicine, there exists a need for health decision algorithms developed through high-level programming languages that already compromised the statistical analyses and numerical computations. Here, we present a tool that enables us to facilitate making research in the PubMed database by classifying the scientific literature from the published abstracts and then performed the comparative analysis to highlight the importance of gene-variant relationships in the decision steps. After retrieving related genes from literature, we performed pathway analysis with them by using computer-based tools to differentiate these sub-pathways in cardiomyopathy disease that are listed as hypertrophic, dilated, and arrhythmogenic right ventricular cardiomyopathy. Then, the pathogenic variants existing in these genes at each sub-pathway are retrieved, and the mechanistic interpretation about them has been gained to explain more about the differences in genes' mode of action. Lastly, the need of structure-based studies to explain the etiology of the disease has been emphasized by providing the protein structures of related genes as a guide. This study presents the importance of combining the text-mining approach with the bioinformatics tool in effective manner both for catching up with the updated literature and for revealing newly identified genes or pathways.</p></div>","PeriodicalId":38190,"journal":{"name":"Meta Gene","volume":"30 ","pages":"Article 100975"},"PeriodicalIF":0.8000,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214540021001262/pdfft?md5=c00d7a2e6df9901b049e31cf9f1aacbb&pid=1-s2.0-S2214540021001262-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Performing the comparative analysis to understand the functional roles of genes in different pathways of cardiomyopathy disease\",\"authors\":\"Evren Atak , Dilara Karaoğlu , Seda Serttürk , Duygu Koyuncu Irmak , Aslı Yenenler-Kutlu\",\"doi\":\"10.1016/j.mgene.2021.100975\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Personalized medicine is one of the popular approaches in biological sciences. Due to the great attention in personalized medicine, there exists a need for health decision algorithms developed through high-level programming languages that already compromised the statistical analyses and numerical computations. Here, we present a tool that enables us to facilitate making research in the PubMed database by classifying the scientific literature from the published abstracts and then performed the comparative analysis to highlight the importance of gene-variant relationships in the decision steps. After retrieving related genes from literature, we performed pathway analysis with them by using computer-based tools to differentiate these sub-pathways in cardiomyopathy disease that are listed as hypertrophic, dilated, and arrhythmogenic right ventricular cardiomyopathy. Then, the pathogenic variants existing in these genes at each sub-pathway are retrieved, and the mechanistic interpretation about them has been gained to explain more about the differences in genes' mode of action. Lastly, the need of structure-based studies to explain the etiology of the disease has been emphasized by providing the protein structures of related genes as a guide. This study presents the importance of combining the text-mining approach with the bioinformatics tool in effective manner both for catching up with the updated literature and for revealing newly identified genes or pathways.</p></div>\",\"PeriodicalId\":38190,\"journal\":{\"name\":\"Meta Gene\",\"volume\":\"30 \",\"pages\":\"Article 100975\"},\"PeriodicalIF\":0.8000,\"publicationDate\":\"2021-12-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2214540021001262/pdfft?md5=c00d7a2e6df9901b049e31cf9f1aacbb&pid=1-s2.0-S2214540021001262-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Meta Gene\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2214540021001262\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Meta Gene","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2214540021001262","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Performing the comparative analysis to understand the functional roles of genes in different pathways of cardiomyopathy disease
Personalized medicine is one of the popular approaches in biological sciences. Due to the great attention in personalized medicine, there exists a need for health decision algorithms developed through high-level programming languages that already compromised the statistical analyses and numerical computations. Here, we present a tool that enables us to facilitate making research in the PubMed database by classifying the scientific literature from the published abstracts and then performed the comparative analysis to highlight the importance of gene-variant relationships in the decision steps. After retrieving related genes from literature, we performed pathway analysis with them by using computer-based tools to differentiate these sub-pathways in cardiomyopathy disease that are listed as hypertrophic, dilated, and arrhythmogenic right ventricular cardiomyopathy. Then, the pathogenic variants existing in these genes at each sub-pathway are retrieved, and the mechanistic interpretation about them has been gained to explain more about the differences in genes' mode of action. Lastly, the need of structure-based studies to explain the etiology of the disease has been emphasized by providing the protein structures of related genes as a guide. This study presents the importance of combining the text-mining approach with the bioinformatics tool in effective manner both for catching up with the updated literature and for revealing newly identified genes or pathways.
Meta GeneBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
1.10
自引率
0.00%
发文量
20
期刊介绍:
Meta Gene publishes meta-analysis, polymorphism and population study papers that are relevant to both human and non-human species. Examples include but are not limited to: (Relevant to human specimens): 1Meta-Analysis Papers - statistical reviews of the published literature of human genetic variation (typically linked to medical conditionals and/or congenital diseases) 2Genome Wide Association Studies (GWAS) - examination of large patient cohorts to identify common genetic factors that influence health and disease 3Human Genetics Papers - original studies describing new data on genetic variation in smaller patient populations 4Genetic Case Reports - short communications describing novel and in formative genetic mutations or chromosomal aberrations (e.g., probands) in very small demographic groups (e.g., family or unique ethnic group). (Relevant to non-human specimens): 1Small Genome Papers - Analysis of genetic variation in organelle genomes (e.g., mitochondrial DNA) 2Microbiota Papers - Analysis of microbiological variation through analysis of DNA sequencing in different biological environments 3Ecological Diversity Papers - Geographical distribution of genetic diversity of zoological or botanical species.