MGI Mouse Gene Expression Database

Abbreviation:GXD

Recommended

General Information

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.

Homepage http://www.informatics.jax.org/expression.shtml

Countries that developed this resource United States

Created in 1998

Taxonomic range

Mus musculus

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: GXD; MGI Mouse Gene Expression Database; DOI: https://doi.org/10.25504/FAIRsharing.q9neh8; Last edited: March 16, 2021, 12:54 p.m.; Last accessed: Apr 12 2021 12:39 a.m.

Publication for citation The mouse Gene Expression Database (GXD): 2021 update. 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; Nucleic Acids Res ; 2020; 10.1093/nar/gkaa914;

This record is maintained by jberghout ORCID

Record added: Jan. 26, 2015, 10:34 a.m.
Record updated: March 16, 2021, 12:06 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.q9neh8' by 'The FAIRsharing Team' at 12:06, 16 Mar 2021 (approved):

	'standardsImplemented' has been modified:
		Before:
			Mouse Adult Gross Anatomy Ontology
			e-Mouse Atlas Project Anatomy Ontology
			Animal Trait Ontology for Livestock
		After:
			Mouse Adult Gross Anatomy Ontology
			e-Mouse Atlas Project Anatomy Ontology
			Animal Trait Ontology for Livestock
			Gene Ontology
			Mammalian Phenotype Ontology
			Disease Ontology
		Added:
			Gene Ontology
			Mammalian Phenotype Ontology
			Disease Ontology
		Removed:

	'related_databases' has been modified:
		Before:
			Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
			MouseMine @ MGI
		After:
			Expression Atlas
			ArrayExpress
			Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
			Gene Expression Omnibus
			MouseMine @ MGI
		Added:
			Expression Atlas
			ArrayExpress
			Gene Expression Omnibus
		Removed:

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.informatics.jax.org/faq/FAQ.shtml
			contact form|http://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml
			help|http://www.informatics.jax.org/mgihome/homepages/help.shtml
		After:
			help|http://www.informatics.jax.org/mgihome/GXD/FirstTimeUsers.shtml
			online documentation|http://www.informatics.jax.org/mgihome/homepages/stats/all_stats.shtml#allstats_gxd
			online documentation|http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml
		Added:
			help|http://www.informatics.jax.org/mgihome/GXD/FirstTimeUsers.shtml
			online documentation|http://www.informatics.jax.org/mgihome/homepages/stats/all_stats.shtml#allstats_gxd
			online documentation|http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml
		Removed:
			FAQ|http://www.informatics.jax.org/faq/FAQ.shtml
			contact form|http://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml
			help|http://www.informatics.jax.org/mgihome/homepages/help.shtml

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Genetics
			Genomics
			Transcriptomics
		Added:
			Genetics
			Genomics
			Transcriptomics
		Removed:
			Life Science

	'onto_domains' has been modified:
		Before:
			Gene expression data
			genome
		After:
			Gene expression data
			Model organisms
			RNA-seq assay
			genome
		Added:
			Model organisms
			RNA-seq assay
		Removed:

	'contact' has been modified:
		Before: 
		After: General Contact

	'miriam_id' has been modified:
		Before: None
		After: 

	'publications' has been modified:
		Before:
			The gene expression database for mouse development (GXD): Putting developmental expression information at your fingertips.|Smith CM, Finger JH, Kadin JA, Richardson JE, Ringwald M.|Developmental Dynamics|2014
			The mouse Gene Expression Database (GXD): 2014 update.|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.|Nucleic Acids Res.|2014
			 The mouse Gene Expression Database (GXD): 2011 update. |Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M.|Nucleic Acids Res 39 (suppl. 1)|2011
			 The mouse Gene Expression Database (GXD): 2007 update. |Smith CM, Finger JH, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald, M.|Nucleic Acids Res. (Database Issue)|2007
			 The Mouse Gene Expression Database (GXD).|Ringwald M, Eppig JT, Begley DA, Corradi JP, McCright IJ, Hayamizu TF, Hill DP, Kadin JA, Richardson JE. |Nucleic Acids Res.|2001
		After:
			The gene expression database for mouse development (GXD): Putting developmental expression information at your fingertips.|Smith CM, Finger JH, Kadin JA, Richardson JE, Ringwald M.|Developmental Dynamics|2014
			The mouse Gene Expression Database (GXD): 2014 update.|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.|Nucleic Acids Res.|2014
			 The mouse Gene Expression Database (GXD): 2011 update. |Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M.|Nucleic Acids Res 39 (suppl. 1)|2011
			 The mouse Gene Expression Database (GXD): 2007 update. |Smith CM, Finger JH, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald, M.|Nucleic Acids Res. (Database Issue)|2007
			 The Mouse Gene Expression Database (GXD).|Ringwald M, Eppig JT, Begley DA, Corradi JP, McCright IJ, Hayamizu TF, Hill DP, Kadin JA, Richardson JE. |Nucleic Acids Res.|2001
			The mouse Gene Expression Database (GXD): 2019 update.|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|Nucleic Acids Res|2018
			The mouse Gene Expression Database (GXD): 2021 update.|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|Nucleic Acids Res|2020
		Added:
			The mouse Gene Expression Database (GXD): 2019 update.|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|Nucleic Acids Res|2018
			The mouse Gene Expression Database (GXD): 2021 update.|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|Nucleic Acids Res|2020
		Removed:

	'dataProcesses' has been modified:
		Before:
			search, data access, http://www.informatics.jax.org/allsearch.shtml
			Download, data access, ftp://ftp.informatics.jax.org/pub/reports/index.html
			Submit, data access, http://www.informatics.jax.org/submit.shtml
		After:
			Search, data access, http://www.informatics.jax.org/gxd
			Download, data release, http://www.informatics.jax.org/downloads/reports/index.html#expression
			Submit, data curation, http://www.informatics.jax.org/mgihome/GXD/GEN/gxd_submission_guidelines.shtml
			Differential Expression Search, data access, http://www.informatics.jax.org/gxd/differential
			Gene List Search, data access, http://www.informatics.jax.org/gxd/batchSearch
			Mouse Developmental Anatomy Browser, data access, http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039
			RNA-Seq and Microarray Search, data access, http://www.informatics.jax.org/gxd/htexp_index
			Literature Search, data access, http://www.informatics.jax.org/gxdlit
			Tissue x Stage Matrix, data access, http://www.informatics.jax.org/gxd/tissue_matrix
		Added:
			Search, data access, http://www.informatics.jax.org/gxd
			Download, data release, http://www.informatics.jax.org/downloads/reports/index.html#expression
			Submit, data curation, http://www.informatics.jax.org/mgihome/GXD/GEN/gxd_submission_guidelines.shtml
			Differential Expression Search, data access, http://www.informatics.jax.org/gxd/differential
			Gene List Search, data access, http://www.informatics.jax.org/gxd/batchSearch
			Mouse Developmental Anatomy Browser, data access, http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039
			RNA-Seq and Microarray Search, data access, http://www.informatics.jax.org/gxd/htexp_index
			Literature Search, data access, http://www.informatics.jax.org/gxdlit
			Tissue x Stage Matrix, data access, http://www.informatics.jax.org/gxd/tissue_matrix
		Removed:
			search, data access, http://www.informatics.jax.org/allsearch.shtml
			Download, data access, ftp://ftp.informatics.jax.org/pub/reports/index.html
			Submit, data access, http://www.informatics.jax.org/submit.shtml

	'accessPoints' has been modified:
		Before:
		After:
			REST|http://www.mousemine.org/mousemine/begin.do#Expression|Mousemine API Access
		Added:
			REST|http://www.mousemine.org/mousemine/begin.do#Expression|Mousemine API Access
		Removed:

	'tools' has been modified:
		Before:
			Batch Query||http://www.informatics.jax.org/batch
			MouseMine||http://www.mousemine.org/mousemine/begin.do
			MGI BioMart||http://biomart.informatics.jax.org/
		After:
		Added:
		Removed:
			Batch Query||http://www.informatics.jax.org/batch
			MouseMine||http://www.mousemine.org/mousemine/begin.do
			MGI BioMart||http://biomart.informatics.jax.org/

In Collections

RDA Covid-19 WG Resources

Support

General

help	Help for First-Time Users
online documentation	Statistics
online documentation	About GXD

Additional Information

Contact

General Contact

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

MGI Data Policies and Disclaimer

Data Release

Download

http://www.informatics.jax.org/downloads/reports/index.html#expression

Data Curation

Submit

http://www.informatics.jax.org/mgihome/GXD/GEN/gxd_submission_guidelin ...

Data Access

Search	http://www.informatics.jax.org/gxd
Differential Expression Search	http://www.informatics.jax.org/gxd/differential
Gene List Search	http://www.informatics.jax.org/gxd/batchSearch
Mouse Developmental Anatomy Browser	http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039
RNA-Seq and Microarray Search	http://www.informatics.jax.org/gxd/htexp_index
Literature Search	http://www.informatics.jax.org/gxdlit
Tissue x Stage Matrix	http://www.informatics.jax.org/gxd/tissue_matrix

REST Web Services

Mousemine API Access

http://www.mousemine.org/mousemine/begin.do#Expression

Publications

The gene expression database for mouse development (GXD): Putting developmental expression information at your fingertips.

Smith CM, Finger JH, Kadin JA, Richardson JE, Ringwald M.
Developmental Dynamics 2014