GEO(Gene Expression Omnibus)是一个公共数据库,储存了大量的基因表达数据,特别是芯片数据(Microarray Data)和RNA-seq数据。在生物信息学领域,分析这些数据对于理解基因的功能、寻找生物标记物和进行疾病相关研究至关重要。本文将介绍如何使用Python处理GEO芯片数据,并提供必要的代码示例帮助读者掌握基
Microarray datasets Microarray data of GSE76427 were downloaded from the Gene Expression Omnibus (Home - GEO - NCBI) database. GSE764267 was conducted by GPL10558 (Illumina HumanHT-12 V4.0 expression beadchip). It contained 115 HCC tissue samples and 52 adjacent non-tumor tissue samples. Out of...
1.GEO(Gene Expression Omnibus)是 NCBI(National Center for Biotechnology Information) 维护的一个 公开基因表达数据存储库,主要收录高通量基因表达数据,包括: 微阵列(Microarray) RNA-seq ChIP-seq A…
# Python处理GEO芯片数据 ## 引言 GEO(Gene Expression Omnibus)是一个公共数据库,储存了大量的基因表达数据,特别是芯片数据(Microarray Data)和RNA-seq数据。在生物信息学领域,分析这些数据对于理解基因的功能、寻找生物标记物和进行疾病相关研究至关重要。本文将介绍如何使用Python处理GEO芯片数据,并提供必要的代码示例...
Johnson WE et al. (2007) Adjusting batch effects in microarray expression data… Leek JT et al. (2012) The sva package for removing batch effects… Ritchie ME et al. (2015) limma powers differential expression analyses… 注:本文代码需根据实际数据调整参数,建议在矫正前后均进行充分的质量控制。
Objective To analyze the microarray expression data of sepsis-related acute respiratory distress syndrome (ARDS) in the Gene Expression Omnibus (GEO) database by bioinformatics methods. To observe the alterations of immune cells in peripheral blood, investigate ...
The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret...
Abstract: Objective Bioinformatics was used to screen key genes during the occurrence and progression of gastric cancer. Methods Two microarray data sets (GSE26899 and GSE65801) from GEO database were included in this analysis. Differentially expressed genes (DEGs) between gastric cancer patients and...
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Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420. ...