GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest - PubMed (original) (raw)
GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest
Constance M Smith et al. Database (Oxford). 2020.
Abstract
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 combined with 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). Database URL: http://www.informatics.jax.org/expression.shtml.
© The Author(s) 2020. Published by Oxford University Press.
Figures
Figure 1
Search. Illustrated is a search for experiments studying gene expression in the skeletal muscle of dystrophin (Dmd) mutants. It takes advantage of two of the curated sample attribute fields: anatomical structure (‘skeletal muscle’) and mutant gene (‘_Dmd_’). Additional curated fields available for searching are developmental stage, strain and sex. Users can also do free text searching of experiment titles and descriptions, as well as search by ArrayExpress or GEO id.
Figure 2
Search return. Pictured is the return for the search in Figure 1. Filters that allow for further refinement of the return are circled. The red arrow indicates the button to access the pop-up sample table (Figure 3; discussed below). The display also includes the annotated experimental variable(s) and study type, as well as link-outs to the data at ArrayExpress and GEO and the publication at PubMed.
Figure 3
Sample table. The sample information is displayed in a pop-up table that can be accessed by using the View button (Figure 2). Samples that match the search criteria (Figure 1) are highlighted in pink. The matching samples are annotated to tissues that are ontological children of the search term skeletal muscle and carry mutations of the dystrophin (Dmd) gene.
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References
- Eppig J.T., Smith C.L., Blake J.A. et al. (2017) Mouse genome informatics (MGI): resources for mining mouse genetic, genomic, and biological data in support of primary and translational research. Methods Mol. Biol., 1488, 47–73. - PubMed
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