KTED：一个基于网络的韩国基因组转座元件综合数据库。

KTED: a comprehensive web-based database for transposable elements in the Korean genome.

作者信息

Lee Jin-Ok, Lee Sejoon, Lee Dongyoon, Hwang Taeyeon, Joe Soobok, Yang Jin Ok, Jeong Jibin, Ohn Jung Hun, Kim Jee Hyun

机构信息

Department of Health Science and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 13605, Republic of Korea.

Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea.

出版信息

Bioinform Adv. 2024 Nov 19;4(1):vbae179. doi: 10.1093/bioadv/vbae179. eCollection 2024.

DOI:10.1093/bioadv/vbae179

PMID:39697868

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11652267/

Abstract

SUMMARY

Transposable elements (TEs), commonly referred to as "mobile elements," constitute DNA segments capable of relocating within a genome. Initially disregarded as "junk DNA" devoid of specific functionality, it has become evident that TEs have diverse influences on an organism's biology and health. The impact of these elements varies according to their location, classification, and their effects on specific genes or regulatory components. Despite their significant roles, a paucity of resources concerning TEs in population-scale genome sequencing remains. Herein, we analyze whole-genome sequencing data sourced from the Korean Genome and Epidemiology Study, encompassing 2500 Korean individuals. To facilitate convenient data access and observation, we developed a web-based database, KTED. Additionally, we scrutinized the differential distributions of TEs across five distinct common disease groups: dyslipidemia, hypertension, diabetes, thyroid disease, and cancer.

AVAILABILITY AND IMPLEMENTATION

https://snubh.shinyapps.io/KTED.

摘要

转座元件（TEs），通常被称为“移动元件”，是能够在基因组内重新定位的DNA片段。最初被视为缺乏特定功能的“垃圾DNA”，但现在已经很明显，TEs对生物体的生物学和健康有多种影响。这些元件的影响因其位置、分类以及对特定基因或调控元件的作用而有所不同。尽管它们具有重要作用，但在群体规模的基因组测序中，关于TEs的资源仍然匮乏。在此，我们分析了来自韩国基因组与流行病学研究的全基因组测序数据，涵盖2500名韩国个体。为了便于数据访问和观察，我们开发了一个基于网络的数据库KTED。此外，我们还研究了TEs在五个不同的常见疾病组中的差异分布：血脂异常、高血压、糖尿病、甲状腺疾病和癌症。