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
Highlights
The mouse Gene Expression Database (GXD) is an searchable database that is freely available online for use by researchers to accelerate progress toward understanding the molecular basis of development and disease (1–3)
We have surveyed all mouse transcription profiling experiments in ArrayExpress, identified those that are within GXD’s scope and curated their sample and experiment attributes using controlled vocabularies and ontologies. These annotations are accessible via the RNA-Seq and Microarray Experiment Search that allows users to quickly and reliably find expression studies of interest in ArrayExpress and Gene Expression Omnibus (GEO), where the expression data itself can be accessed
Experiments downloaded from ArrayExpress Experiments incompatible with GXD’s scope∗ Experiments lacking publication required to identify allele used Experiments consistent with GXD’s scope/metadata included in index WT vs mutant studies Baseline studies
Summary
The mouse Gene Expression Database (GXD) is an searchable database that is freely available online for use by researchers to accelerate progress toward understanding the molecular basis of development and disease (1–3). For our first foray into high-throughput expression data, GXD has sought to fulfill a critical, previously unmet community need: to enable researchers to reliably find mouse RNA-seq and microarray studies in the public repositories that are within GXD’s scope. To do this we have developed a sample and experiment metadata index and search tool for these studies.
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