The mouse Gene Expression Database (GXD): 2014 update

D818–D824 Nucleic Acids Research, 2014, Vol. 42, Database issue doi:10.1093/nar/gkt954 Published online 25 October 2013 The mouse Gene Expression Database (GXD): 2014 update Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, Joanne Berghout, Jeff Campbell, Lori E. Corbani, Kim L. Forthofer, Pete J. Frost, Dave Miers, David R. Shaw, Kevin R. Stone, Janan T. Eppig, James A. Kadin, Joel E. Richardson and Martin Ringwald* The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA Received September 12, 2013; Accepted September 26, 2013 ABSTRACT The Gene Expression Database (GXD; http://www. informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. GXD collects different types of expression data from studies of wild-type and mutant mice, covering all developmental stages and including data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. The data are acquired from the scientific literature and from researchers, including groups doing largescale expression studies. Integration with the other data in Mouse Genome Informatics (MGI) and interconnections with other databases places GXD’s gene expression information in the larger biological and biomedical context. Since the last report, the utility of GXD has been greatly enhanced by the addition of new data and by the implementation of more powerful and versatile search and display features. Web interface enhancements include the capability to search for expression data for genes associated with specific phenotypes and/or human diseases; new, more interactive data summaries; easy downloading of data; direct searches of expression images via associated metadata; and new displays that combine image data and their associated annotations. At present, GXD includes >1.4 million expression results and 250 000 images that are accessible to our search tools. INTRODUCTION The laboratory mouse serves as a premier animal model in studying the complex molecular mechanisms that underlie the processes of human development, differentiation and disease. Tissues from all stages of mouse development and from many different mouse strains and mutants are being subjected to detailed expression analysis. The Gene Expression Database (GXD) collects these data from disparate sources, integrates them and makes them readily accessible to many types of biologically and biomedically relevant database searches. By capturing multiple types of mRNA and protein expression information, including data from RNA in situ hybridization, immunohistochemistry, in situ reporter (knock in), reverse transcriptase-polymerase chain reaction (RT-PCR), northern blot and western blot experiments, GXD aims to provide increasingly complete information about where, when and in what amounts transcripts and proteins are expressed during development, as well as how their expression varies in different mouse strains and mutants. Data are acquired from the literature and from researchers, in particular from groups doing large-scale expression studies. All these data are annotated by GXD curators, making extensive use of controlled vocabularies and ontologies to provide the standardization of data that enables data integration and thereby complex queries. GXD forms an integral component of the larger Mouse Genome Informatics (MGI) resource. Through this association, the expression data can be combined with extensive genetic, functional, phenotypic and disease-orientated data (1). This robust integration, as well as interconnections with other resources (2–16), puts the expression data in GXD into a much larger analytical context. Owing to its broad scope, thorough approach, data integration and querying capabilities, GXD provides an important and unique resource to the research community. GXD and its user interfaces have been described previously (17–20). Here we focus on recent progress in terms of data acquisition and improvements to the querying capabilities and web displays. *To whom correspondence should be addressed. Tel: +1 207 288 6436; Fax: +1 207 288 6132; Email: ß The Author(s) 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Research, 2014, Vol. 42, Database issue DATA CONTENT AND PROGRESS IN DATA ACQUISITION Detailed expression data GXD provides detailed records of expression results. The core entry is an assay details record (Figure 1). Each assay details record includes information about the gene studied, the probes and experimental conditions used, the specimen(s) analyzed, the expression results obtained for each specimen, as well as images of the data when available. These data are annotated using standard nomenclature and ontologies and serve as D819 integration points within the GXD and MGI database. Expression patterns are described using an extensive, hierarchically structured anatomical ontology. As well as allowing for the integration of expression results from assays with differing spatial resolution, the hierarchical nature of the ontology allows expression searches by anatomical term to include all substructures for the term. The developmental portion of the anatomical ontology was begun by our collaborators from the eMouseAtlas project (21) and is being extended and refined jointly with GXD; the postnatal part was developed by the GXD project (22). Figure 1. GXD assay details pages contain detailed expression annotations. This record for an RNA in situ hybridization assay illustrates the details included in GXD annotations of expression results. The Assay section reports the reference from which the data were derived, the assay type and the gene analyzed. Details regarding the nucleotide probe (or antibody) used in the assay can be accessed via the link on the page. In the ‘Results’ section, the Theiler stage and tissue examined, as well as the strength and pattern of expression as described by the author, are reported. (If this were a blot assay, the number and sizes of detected bands would also be reported.) Images of the original expression data are displayed beside the annotations describing them, allowing them to be reviewed in context. Major specimen details, such as the age and mutant alleles, are always displayed on the page. Other details, such as genetic background, sex and preparation method, can be viewed by using the ‘more’ toggle to expand that portion of the page. Assay details pages are accessed from the GXD data summaries. D820 Nucleic Acids Research, 2014, Vol. 42, Database issue Table 1. Data content in GXD as of 4 September 2013 15 051 13 767 64 174 1 401 (...truncated)