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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. The mouse Gene Expression Database (GXD): 2021 update. Nucleic Acids Res 2021; 49:D924-D931. [PMID: 33104772 PMCID: PMC7778941 DOI: 10.1093/nar/gkaa914] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 01/05/2023] Open
Abstract
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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Affiliation(s)
| | | | | | - Terry F Hayamizu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jingxia Xu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - David R Shaw
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jonathan S Beal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Olin Blodgett
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jeffrey Campbell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Lori E Corbani
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Pete J Frost
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Dave B Miers
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Martin Ringwald
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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Smith CM, Kadin JA, Baldarelli RM, Beal JS, Blodgett O, Giannatto SC, Richardson JE, Ringwald M. GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. Database (Oxford) 2021; 2020:5756137. [PMID: 32140729 PMCID: PMC7058436 DOI: 10.1093/database/baaa002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/28/2022]
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
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Affiliation(s)
| | - James A Kadin
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
| | | | - Jonathan S Beal
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
| | - Olin Blodgett
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
| | | | | | - Martin Ringwald
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
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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. The mouse Gene Expression Database (GXD): 2019 update. Nucleic Acids Res 2020; 47:D774-D779. [PMID: 30335138 PMCID: PMC6324054 DOI: 10.1093/nar/gky922] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments in wild-type and mutant mice. GXD's gene expression information is integrated with the other data in Mouse Genome Informatics and interconnected with other databases, placing these data in the larger biological and biomedical context. Since the last report, the ability of GXD to provide insights into the molecular mechanisms of development and disease has been greatly enhanced by the addition of new data and by the implementation of new web features. These include: improvements to the Differential Gene Expression Data Search, facilitating searches for genes that have been shown to be exclusively expressed in a specified structure and/or developmental stage; an enhanced anatomy browser that now provides access to expression data and phenotype data for a given anatomical structure; direct access to the wild-type gene expression data for the tissues affected in a specific mutant; and a comparison matrix that juxtaposes tissues where a gene is normally expressed against tissues, where mutations in that gene cause abnormalities.
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Affiliation(s)
| | - Terry F Hayamizu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Susan M Bello
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jingxia Xu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jonathan S Beal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jeffrey Campbell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Lori E Corbani
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Pete J Frost
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jill R Lewis
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Dave Miers
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - David R Shaw
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Cynthia L Smith
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Martin Ringwald
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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Eppig JT, Bult CJ, Kadin JA, Richardson JE, Blake JA, Anagnostopoulos A, Baldarelli RM, Baya M, Beal JS, Bello SM, Boddy WJ, Bradt DW, Burkart DL, Butler NE, Campbell J, Cassell MA, Corbani LE, Cousins SL, Dahmen DJ, Dene H, Diehl AD, Drabkin HJ, Frazer KS, Frost P, Glass LH, Goldsmith CW, Grant PL, Lennon-Pierce M, Lewis J, Lu I, Maltais LJ, McAndrews-Hill M, McClellan L, Miers DB, Miller LA, Ni L, Ormsby JE, Qi D, Reddy TBK, Reed DJ, Richards-Smith B, Shaw DR, Sinclair R, Smith CL, Szauter P, Walker MB, Walton DO, Washburn LL, Witham IT, Zhu Y. The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology. Nucleic Acids Res 2005; 33:D471-5. [PMID: 15608240 PMCID: PMC540067 DOI: 10.1093/nar/gki113] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.
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Affiliation(s)
- Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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Bult CJ, Blake JA, Richardson JE, Kadin JA, Eppig JT, Baldarelli RM, Barsanti K, Baya M, Beal JS, Boddy WJ, Bradt DW, Burkart DL, Butler NE, Campbell J, Corey R, Corbani LE, Cousins S, Dene H, Drabkin HJ, Frazer K, Garippa DM, Glass LH, Goldsmith CW, Grant PL, King BL, Lennon-Pierce M, Lewis J, Lu I, Lutz CM, Maltais LJ, McKenzie LM, Miers D, Modrusan D, Ni L, Ormsby JE, Qi D, Ramachandran S, Reddy TBK, Reed DJ, Sinclair R, Shaw DR, Smith CL, Szauter P, Taylor B, Vanden Borre P, Walker M, Washburn L, Witham I, Winslow J, Zhu Y. The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res 2004; 32:D476-81. [PMID: 14681461 PMCID: PMC308859 DOI: 10.1093/nar/gkh125] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.
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Affiliation(s)
- Carol J Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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