The mouse Gene Expression Database (GXD): 2017 update

D730–D736 Nucleic Acids Research, 2017, Vol. 45, Database issue doi: 10.1093/nar/gkw1073 Published online 28 November 2016 The mouse Gene Expression Database (GXD): 2017 update Jacqueline H. Finger, Constance M. Smith, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, Meiyee Law, David R. Shaw, Richard M. Baldarelli, Jon S. Beal, Olin Blodgett, Jeff W. Campbell, Lori E. Corbani, Jill R. Lewis, Kim L. Forthofer, Pete J. Frost, Sharon C. Giannatto, Lucie N. Hutchins, Dave B. Miers, Howie Motenko, 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 14, 2016; Revised October 21, 2016; Editorial Decision October 24, 2016; Accepted October 28, 2016 The Gene Expression Database (GXD; www. informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. At present, GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata. Since our last report in 2014, we have added a large amount of data, we have enhanced data and database infrastructure, and we have implemented many new search and display features. Interface enhancements include: a new Mouse Developmental Anatomy Browser; interactive tissueby-developmental stage and tissue-by-gene matrix views; capabilities to filter and sort expression data summaries; a batch search utility; gene-based expression overviews; and links to expression data from other species. INTRODUCTION Developmental gene expression information from wild-type and mutant mice provides crucial insights into the molecular mechanisms of human development, differentiation and disease. The longstanding objective of GXD has been to capture and integrate these complex and heterogeneous expression data, generated by many laboratories and scattered through thousands of publications, and to make them readily accessible to researchers via biologically and biomedically relevant searches. Designed from the beginning as an open-ended system that can robustly integrate different types of expression data, GXD collects RNA and protein expression information from RNA in situ hybridization, immunohistochemistry, in situ reporter (knock in), RT-PCR, northern blot, and western blot experiments (1,2). Data are acquired from the literature and through collaboration with projects that generate the types of data GXD collects at a large scale. All these data are reviewed and annotated by GXD Curators in standardized ways by making extensive use of controlled vocabularies and ontologies. As an integral component of the larger Mouse Genome Informatics (MGI) resource (3–5), GXD combines the expression data with genetic, functional, phenotypic, and disease-oriented data, thereby enabling unique and powerful search capabilities. GXD and its user interfaces have been described previously (6,7). Here, we focus on progress made since our last report in the NAR Database Issue (8). DATA CONTENT AND PROGRESS IN DATA ACQUISITION Comprehensive literature survey We systematically survey journals to find all publications examining endogenous gene expression during mouse development. In a first curation step for each paper, we annotate the genes and ages analyzed and the expression assay types used. Annotations are based on the entire publication, including supplemental information, and employ official nomenclature for genes. This information, combined with bibliographic information from PubMed, is made available for searches via the Gene Expression Literature Query form (http://www.informatics.jax.org/gxdlit). GXD’s liter- * To whom correspondence should be addressed. Tel: +1 207 288 6436; Fax: +1 207 288 6830; Email:  C The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact ABSTRACT Nucleic Acids Research, 2017, Vol. 45, Database issue D731 Figure 1. The Assay Details Page––annotated expression data are displayed with citation information, gene, and experimental information, such as the assay type, probe visualization method and link to probe specifics. The results section of the page includes the level and pattern of expression in anatomical structures (annotated using the Mouse Developmental Anatomy Ontology). Image panes accompany the result annotations when available. The pane can be viewed in the context of the full figure by clicking on the image or the link in the result table. Specimen information includes the age, genetic background and specimen preparation methods. Further details can be viewed by expanding the ‘more’ toggle (boxed region indicated by red circle & arrow). If the specimen is from a mutant mouse, the official allele name is shown with links to all the information for that allele in MGI, including all the other expression data for this specific mouse mutant. ature content records are comprehensive and up-to-date from 1990 to the present. GXD has records for over 24 300 references and >15 500 genes. The Gene Expression Literature Query provides researchers with an effective tool for finding publications with specific expression data, and it helps GXD Curators to prioritize papers for detailed expression annotation. Detailed expression data In a second curation step, the expression data are annotated in detail. For each expression assay, we record information about the gene studied, the strength and pattern of expression in specific anatomical structures, the probes and experimental conditions used, and the age and genetic background of the specimen(s) analyzed. Images of the data accompany the annotations when available. Standard gene, D732 Nucleic Acids Research, 2017, Vol. 45, Database issue Figure 2. The Mouse Developmental Anatomy Browser––divided into three sections, the Anatomy Search, the Anatomical Term Detail and the Anatomical Tree View, the user can quickly find terms and explore the mouse anatomy ontology. As indicated in the Term Detail section, individual structures can have multiple parents; ‘branchial arch endoderm’ has Parent Terms ‘embryo endoderm’ (...truncated)