European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK.
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Nucleic Acids Res. 2022 Jan 7;50(D1):D129-D140. doi: 10.1093/nar/gkab1030.
The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from >4500 expression studies from >65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools. Each study's metadata are annotated using ontologies. The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas. Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to Single Cell RNA-Sequencing (scRNA-Seq) studies. The resource has been in continuous development since 2009 and it is available at https://www.ebi.ac.uk/gxa.
EMBL-EBI Expression Atlas 是一个增值知识库，使研究人员能够回答基因或感兴趣的蛋白质在何处（组织、生物体部分、发育阶段、细胞类型）和在何种条件下（疾病、治疗、性别等）表达的问题。Expression Atlas 将来自超过 65 个不同物种的 >4500 个表达研究的数据汇集在一起，涵盖了不同的条件和组织。它以易于可视化的形式免费提供这些数据，经过专家精心整理，以准确代表预期的实验设计，并通过依赖开源社区开发工具的标准化管道进行重新分析。每个研究的元数据都使用本体进行注释。数据被重新分析，旨在重现基础实验的原始结论。Expression Atlas 目前分为 Bulk Expression Atlas 和 Single Cell Expression Atlas。Expression Atlas 包含来自差异研究（微阵列和批量 RNA-Seq）和基线研究（批量 RNA-Seq 和蛋白质组学）的数据，而 Single Cell Expression Atlas 目前专门用于单细胞 RNA 测序 (scRNA-Seq) 研究。该资源自 2009 年以来一直在不断开发，可在 https://www.ebi.ac.uk/gxa 上获得。
