数据库|HRGFish:鱼类缺氧基因数据库

HRGFish: A database of hypoxia responsive genes in fishes3.998Sci Rep . 2017 Feb 13;7:42346. doi: 10.1038/srep42346.

Abstract

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

由于水温升高、有机物污染或有消耗氧气的水生植物存在引起的水体缺氧，是鱼类经常受到的一种非生物胁迫。缺氧会直接影响鱼类的生理和细胞功能，因此了解鱼类的低氧耐受性是十分重要的。

目前已经开展了多项关于鱼类低氧耐受性的研究，鲤科、斑马鱼、虹鳟等物种的低氧适应性机制都有报告。研究人员采用了多种方法鉴定鱼类中缺氧反应基因及表达水平的变化，发现缺氧诱导因子（HIF）及其在低氧条件下基因调控中的作用。HIF是一种高度保守的异二聚体，由蛋白质链的α和β亚基组成，可对细胞环境中的氧张力变化做出响应。由于鱼类低氧条件下的进化适应性并不统一，多项研究鉴定出了许多缺氧反应相关的基因，但目前还缺乏一个能够收集、管理这些基因及基因信息的平台。

基于这一目的，Mahender Singh等人开发了鱼类缺氧反应基因数据库HRGFish（http://mail.nbfgr.res.in/HRGFish），成果于2017年发表在《Scientific Reports》上。

数据库收录了38种鱼类的35种缺氧反应基因，具有可视化界面，集成了用于上下游分析、引物设计、序列相似性和关键词检索的工具，有助于理解基因调控、调控元件、缺氧反应元件（HRE）方向、耐受性和物种对缺氧的敏感性。便于研究者了解缺氧反应中细胞适应性，同时也填补了种内种间遗传变异在缺氧耐受性中的作用方面的知识空白。

HRGFish的体系结构和数据流程图

HRE（缺氧反应元件）分析页面：显示IGFBP1基因直系同源组中的所有HRE