GEO数据库架构、申请及数据提取方法与流程
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摘要
基因表达综合数据库(Gene Expression Omnibus),简称GEO数据库,由美国生物技术信息中心(NCBI)开发的一个完全公开的高通量基因分子丰度数据库,是一个公共功能基因组数据存储库,接受基于数组和序列的数据。该数据库主要储存基因表达数据,涵盖多个生物学领域的高通量实验数据,其提供工具帮助用户查询和下载实验和管理基因表达谱,为生物信息学研究提供了大量与疾病相关的基因表达谱信息。研究者通过对基因芯片提供的大量基因表达谱数据信息的深度挖掘和分析,有助于了解基因的功能以及基因间的相互作用关系,解读基因表达的代谢过程,分析基因的遗传特征和功能,研究疾病的发生发展规律,为疾病的诊断与治疗提供科学参考。本文旨在介绍GEO数据库的架构、申请方式及公开数据的提取方法。
Gene Expression Omnibus, referred to as the GEO database, is a fully publicized high-throughput gene molecular abundance database developed by the Center for Biotechnology Information(NCBI). It is a public functional genomic data repository that accepts array-and sequence-based data. The database stores gene expression data covering high-throughput experimental data from multiple biological fields. It provides tools to help users query and download experiments and manage gene expression profiles, providing a wealth of disease-related gene expression profiles for bioinformatics research. Through deep mining and analysis of gene expression data information provided by gene chips, researchers can understand the function of genes and the interactions between genes, interpret the metabolic processes of gene expression, and analyze the genetic characteristics and functions of genes, to study the law of the occurrence and development of diseases, and provide scientific reference for the diagnosis and treatment of diseases.This article aims to introduce the architecture of the GEO database, how to apply it, and how to extract public data.
Gene Expression Omnibus, referred to as the GEO database, is a fully publicized high-throughput gene molecular abundance database developed by the Center for Biotechnology Information(NCBI). It is a public functional genomic data repository that accepts array-and sequence-based data. The database stores gene expression data covering high-throughput experimental data from multiple biological fields. It provides tools to help users query and download experiments and manage gene expression profiles, providing a wealth of disease-related gene expression profiles for bioinformatics research. Through deep mining and analysis of gene expression data information provided by gene chips, researchers can understand the function of genes and the interactions between genes, interpret the metabolic processes of gene expression, and analyze the genetic characteristics and functions of genes, to study the law of the occurrence and development of diseases, and provide scientific reference for the diagnosis and treatment of diseases.This article aims to introduce the architecture of the GEO database, how to apply it, and how to extract public data.
引文
[1]胡国兴,余晓茹.基于GEO数据库的胃癌耐药基因表达谱分析及其对预后的影响[J].实用癌症杂志,2018,33(1):10-3.
[2]余海浪,马文丽,郑文岭.用于基因数据挖掘的基因表达数据库GEO[J].中国生物工程杂志,2007,(8):96-103.
[3]周大琼,曹继华,任力锋,等.基因芯片数据库GEO与ArrayExpress的使用及比较分析[J].中国现代医学杂志,2014,24(12):38-42.
[4]王维,林雷,郭敏,等.基于基因表达数据库的鼠ZFP580基因功能分析[J].武警医学院学报,2011,20(2):147-50.
[5]钟要红,何青芳,李迎君,等.基于GEO芯片数据库的结肠癌易感基因挖掘[J].预防医学,2017,29(11):1094-7.
[6]熊筱晶. GEO基因表达数据库中芯片技术平台的统计分析[J].生命的化学,2009,29(1):115-9.
[7]张轶雯,楼倩雯,钟里科,等.基于GEO数据库的近端与远端结肠癌特征基因生物信息学研究[J].中国临床药理学与治疗学,2018,23(4):422-7.
[8]张阁.基于GEO数据库的差异表达基因分析系统的构建[D].山西医科大学,2018.
[2]余海浪,马文丽,郑文岭.用于基因数据挖掘的基因表达数据库GEO[J].中国生物工程杂志,2007,(8):96-103.
[3]周大琼,曹继华,任力锋,等.基因芯片数据库GEO与ArrayExpress的使用及比较分析[J].中国现代医学杂志,2014,24(12):38-42.
[4]王维,林雷,郭敏,等.基于基因表达数据库的鼠ZFP580基因功能分析[J].武警医学院学报,2011,20(2):147-50.
[5]钟要红,何青芳,李迎君,等.基于GEO芯片数据库的结肠癌易感基因挖掘[J].预防医学,2017,29(11):1094-7.
[6]熊筱晶. GEO基因表达数据库中芯片技术平台的统计分析[J].生命的化学,2009,29(1):115-9.
[7]张轶雯,楼倩雯,钟里科,等.基于GEO数据库的近端与远端结肠癌特征基因生物信息学研究[J].中国临床药理学与治疗学,2018,23(4):422-7.
[8]张阁.基于GEO数据库的差异表达基因分析系统的构建[D].山西医科大学,2018.
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