The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. The project is funded byNIH/NICHD grant HD062499.
New expression data are made available on a weekly basis. These data are acquired from the literature by our curatorial staff and via electronic submission. GXD encourages researchers to submit their expression data to us. Data submission both increases the exposure of the work and the amount of data available to the scientific community. Guidelines for submitting data can be found here.
We have incorporated data from several large scale expression databases into GXD. Database entries in GXD may link to the corresponding entries at the providers' websites. In this way, users can take advantage of GXD's data integration and querying capabilities while having easy access to additional resources at the providers' sites.
We have also incorporated directly submitted data from the following major studies:
Selected sets of RNA-seq data are imported from the EMBL-EBI's Expression Atlas. These data are from experiments that examine endogenous gene expression in wild-type and mutant mice during the embryonic stages and/or postnatal life. In keeping with GXD's scope, we do not select data derived from transgenic mice (i.e., animals containing randomly inserted transgenes); animals that have been manipulated, either by substances, surgical procedures, or diet regimens; cultured tissues; cell types; or cell lines.
We chose the Expression Atlas as our data source because their team selects high quality data sets from the public repositories (ArrayExpress and NCBI's GEO) and then uses a standardized pipeline to re-analyze the data, generating consistently processed TPM values. To effectively integrate these data into GXD, we process and annotate these files further:
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 2021. The mouse Gene Expression Database (GXD): 2021 update. Nucleic Acids Res. 2021 Jan 8;49(D1):D924-D931. PubMed
Smith CM, Kadin JA, Baldarelli RM, Beal JS, Blodgett O, Giannatto SC, Richardson JE, Ringwald M 2020. GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. Database 2020 Mar. 4 PubMed
Smith CM, Hayamizu TF, Finger JH, Bello SM, McCright IJ, Xu J, Baldarelli RM, Beal JS, Campbell JW, Corbani LE, Frost PJ, Lewis, JR, Giannatto SC, Miers DB, Shaw DR, Kadin JA, Richardson JE, Smith CL, Ringwald M. 2019. The mouse Gene Expression Database (GXD): 2019 update. Nucleic Acids Res. 2019 Jan. 8;47 (D1): D774–D779. PubMed
Finger JH, Smith CM, Hayamizu TF, McCright IJ, Xu J, Law M, Shaw DR, Baldarelli RM, Beal JS, Blodgett O, Campbell JW, Corbani LE, Lewis JR, Forthofer KL, Frost PJ, Giannatto SC, Hutchins LN, Miers DB, Motenko H, Stone KR, Eppig JT, Kadin JA, Richardson JE, Ringwald M. 2017. The mouse Gene Expression Database (GXD): 2017 update. Nucleic Acids Res. 2017 Jan. 4;45 (D1): D730-D736. PubMed
Hayamizu TF, Baldock RA, Ringwald M. 2015. Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. Mamm Genome. 2015 Oct;26(9-10):422-30. PubMed
Smith CM, Finger JH, Hayamizu TF, McCright IJ, Xu J, Eppig JT, Kadin JA, Richardson JE, Ringwald M. 2015. GXD: a community resource of mouse Gene Expression Data. Mamm Genome. 2015 Aug;26(7):314-324. PubMed
Finger JH, Smith CM, Hayamizu TF, McCright IJ, Xu J, Eppig JT, Kadin JA, Richardson JE, Ringwald M. 2015. The mouse gene expression database: New features and how to use them effectively. Genesis. doi: 10.1002/dvg.22864. PubMed
Smith CM, Finger JH, Kadin JA, Richardson JE, Ringwald M. The gene expression database for mouse development (GXD): Putting developmental expression information at your fingertips. 2014. DevDyn Oct;243(10):1176-1186. PubMed
Smith CM, Finger JH, Hayamizu TF, McCright IJ, Xu J, Berghout J, Campbell J, Corbani LE, Forthofer KL, Frost PJ, Miers D, Shaw DR, Stone KR, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2014 update. Nucleic Acids Res. 2014 Jan 1;42(D1):D818-D824. NAR PubMed
Hayamizu TF, Wicks MN, Davidson DR, Burger A, Ringwald M, Baldock RA. EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. J Biomed Semantics. 2013 Aug 26;4(1):15. PubMed
Ringwald M, Wu C, Su AI. BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. Mamm Genome. 2012 Oct;23(9-10):550-8. PubMed
Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res 39(suppl 1): D835-D841. NAR PubMed
Smith CM, Finger JH, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald, M. The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res 2007 35(Database issue):D618-D623. NAR PubMed
Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M. The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol, 2005;6:R29 PubMed.
Hill DP, Begley DA, Finger JH, Hayamizu TF, McCright IJ, Smith CM, Beal JS, Corbani LE, Blake JA, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The Mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res 2004; 32:D568-D571. NARPubMed
Begley DA, Ringwald M. 2002. Electronic tools to manage gene expression data. Trends Genet 18:108-110.
Ringwald M, Eppig JT, Begley DA, Corradi JP, McCright IJ, Hayamizu TF, Hill DP, Kadin JA, Richardson JE. 2001. The Mouse Gene Expression Database (GXD). Nucleic Acids Res 29:98-101. PubMed
Ringwald M, Eppig JT, Richardson JE. 2000. GXD: integrated access to gene expression data for the laboratory mouse. Trends Genet 16:188-190.PubMed
Bard JBL, Kaufman MH, Dubreuil C, Brune RM, Burger A, Baldock RA and Davidson DR. 1998. An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech Dev 74:111-120.
Ringwald M, Baldock R, Bard J, Kaufmann M, Eppig JT, Richardson JE, Nadeau JH, Davidson D. 1994. A database for mouse development. Science 265: 2033-2034.PubMed
