Department of Pharmacological Sciences; Mount Sinai Center for Bioinformatics; Big Data to Knowledge, Library of Integrated Network-based Cellular Signatures, Data Coordination and Integration Center (BD2K-LINCS DCIC); Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY, 10029, USA.
Nat Commun. 2018 Apr 10;9(1):1366. doi: 10.1038/s41467-018-03751-6.
RNA sequencing (RNA-seq) is the leading technology for genome-wide transcript quantification. However, publicly available RNA-seq data is currently provided mostly in raw form, a significant barrier for global and integrative retrospective analyses. ARCHS4 is a web resource that makes the majority of published RNA-seq data from human and mouse available at the gene and transcript levels. For developing ARCHS4, available FASTQ files from RNA-seq experiments from the Gene Expression Omnibus (GEO) were aligned using a cloud-based infrastructure. In total 187,946 samples are accessible through ARCHS4 with 103,083 mouse and 84,863 human. Additionally, the ARCHS4 web interface provides intuitive exploration of the processed data through querying tools, interactive visualization, and gene pages that provide average expression across cell lines and tissues, top co-expressed genes for each gene, and predicted biological functions and protein-protein interactions for each gene based on prior knowledge combined with co-expression.
RNA 测序（RNA-seq）是全基因组转录物定量的领先技术。然而，目前公开可用的 RNA-seq 数据主要以原始形式提供，这是全球和综合回顾性分析的一个重大障碍。ARCHS4 是一个网络资源，可提供人类和小鼠的大多数已发表的 RNA-seq 数据，可在基因和转录本水平上使用。为了开发 ARCHS4，使用基于云的基础架构对来自基因表达综合数据库（GEO）的 RNA-seq 实验的可用 FASTQ 文件进行了对齐。通过 ARCHS4 可访问 187946 个样本，其中包括 103083 个小鼠样本和 84863 个人类样本。此外，ARCHS4 网络界面通过查询工具、交互式可视化和基因页面提供经过处理的数据的直观探索，这些工具提供了跨细胞系和组织的平均表达、每个基因的顶级共表达基因以及基于先前知识与共表达相结合的每个基因的预测生物学功能和蛋白质-蛋白质相互作用。
