GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest
GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest
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DOI：
10.1093/database/baaa002
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发表时间：
2020-03-04
影响因子：
5.8
通讯作者：
Ringwald, Martin
中科院分区：
文献类型：
--
作者：
Smith, Constance M.;Kadin, James A.;Ringwald, Martin
基因表达数据库（GXD）是一个广泛的小鼠组织表达信息的社区资源，已经开发了RNA-Seq和微阵列实验搜索（http：//www.informatics.jax.org/gxd/htexp_index）。该工具允许用户快速可靠地在ArrayExpress和基因表达综合系统（GEO）中找到研究野生型和突变小鼠内源基因表达的特定实验。由GXD策划的标准化元数据注释允许用户指定感兴趣样本的解剖结构、发育阶段、突变基因、品系和性别，以及实验的研究类型和关键参数。这些搜索由受控词汇和本体驱动，可以与实验标题和描述的自由文本搜索相结合。搜索结果摘要包括到ArrayExpress和GEO的链接，提供对表达式数据本身的轻松访问。链接到PubMed条目随附出版物也包括在内。有关此工具和GXD的更多信息，请访问GXD主页（http：//www. informatics.jax.org/ comexpression.shtml）。
The Gene Expression Database (GXD), an extensive community resource of curated expression information for the mouse, has developed an RNA-Seq and Microarray Experiment Search (http://www.informatics.jax.org/gxd/htexp_index). This tool allows users to quickly and reliably find specific experiments in ArrayExpress and the Gene Expression Omnibus (GEO) that study endogenous gene expression in wild-type and mutant mice. Standardized metadata annotations, curated by GXD, allow users to specify the anatomical structure, developmental stage, mutated gene, strain and sex of samples of interest, as well as the study type and key parameters of the experiment. These searches, powered by controlled vocabularies and ontologies, can be combinedwith free text searching of experiment titles and descriptions. Search result summaries include link-outs to ArrayExpress and GEO, providing easy access to the expression data itself. Links to the PubMed entries for accompanying publications are also included. More information about this tool and GXD can be found at the GXD home page (http://www. informatics.jax.org/ expression.shtml).