The mouse Gene Expression Database (GXD): 2021 update.
The mouse Gene Expression Database (GXD): 2021 update.
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DOI：
10.1093/nar/gkaa914
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Ringwald M
中科院分区：
文献类型：
--
作者：
Baldarelli RM;Smith CM;Finger JH;Hayamizu TF;McCright IJ;Xu J;Shaw DR;Beal JS;Blodgett O;Campbell J;Corbani LE;Frost PJ;Giannatto SC;Miers DB;Kadin JA;Richardson JE;Ringwald M
基因表达数据库(GXD；www.informatics.jax.org/pression.shtml)是一个广泛和精心策划的关于小鼠发育基因表达信息的社区资源。多年来，GXD通过科学文献的整理和与大型表达项目的合作，从RNA原位杂交、免疫组织化学、RT-PCR、Northern印迹和Western印迹实验中收集和整合了数据。自从我们在2019年发布上一份报告以来，我们继续获取这些经典类型的表达数据；开发了可搜索的RNA-Seq和微阵列实验索引，使用户能够快速可靠地在ArrayExpress(https://www.ebi.ac.uk/arrayexpress/)和Geo(https://www.ncbi.nlm.nih.gov/geo/)；)和扩展的GXD中找到特定的鼠标表达研究，以包括RNA-Seq数据。统一处理的RNA-Seq数据从EBI表达图谱中导入，然后与GXD中的其他类型的表达数据以及小鼠基因组信息学(MGI)中的遗传、功能、表型和疾病相关信息集成。这种集成使人们可以通过GXD增强的搜索和过滤功能访问RNA-Seq数据。此外，我们还将Morpheus热图实用程序嵌入到GXD用户界面中，以提供用于显示和分析RNA-Seq数据的其他工具，包括热图可视化、排序、过滤、层次聚类、最近邻分析和可视化丰富。
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD’s enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment.
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DOI：
10.1002/dvg.22864
发表时间：
2015-08
期刊：
Genesis (New York, N.Y. : 2000)
影响因子：
--
作者：
Finger JH;Smith CM;Hayamizu TF;McCright IJ;Xu J;Eppig JT;Kadin JA;Richardson JE;Ringwald M
通讯作者：
Ringwald M
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
影响因子：
2.5
作者：
Drabkin, Harold J.;Christie, Karen R.;Blake, Judith A.
通讯作者：
Blake, Judith A.
DOI：
10.1093/database/baaa002
发表时间：
2020-03-04
影响因子：
5.8
作者：
Smith, Constance M.;Kadin, James A.;Ringwald, Martin
通讯作者：
Ringwald, Martin
影响因子：
14.9
作者：
Smith CM;Hayamizu TF;Finger JH;Bello SM;McCright IJ;Xu J;Baldarelli RM;Beal JS;Campbell J;Corbani LE;Frost PJ;Lewis JR;Giannatto SC;Miers D;Shaw DR;Kadin JA;Richardson JE;Smith CL;Ringwald M
通讯作者：
Ringwald M