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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 (+5 others)
2013 Nucleic Acids Research  
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.  ...  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.  ...  ACKNOWLEDGEMENTS We would like to thank our colleagues from the other MGI projects for their contributions to the GXD project and to the larger MGI resource.  ... 
doi:10.1093/nar/gkt954 pmid:24163257 pmcid:PMC3965015 fatcat:eogjmum57rcurgukgaz4hdqaq4

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

Constance M. Smith, Jacqueline H. Finger, James A. Kadin, Joel E. Richardson, Martin Ringwald
2014 Developmental Dynamics  
Using the Gene Expression Database for Mouse Development (GXD) as an example, we illustrate the progress made towards this goal, and discuss relevant issues that apply to developmental databases and developmental  ...  Here we describe the data and search tools of GXD; explain how to use the database most effectively; discuss how we acquire, curate, and integrate developmental expression information; and describe how  ...  Acknowledgments We would like to thank our colleagues from the GXD project, as well as our colleagues from other MGI projects for their contributions to GXD and the larger MGI resource.  ... 
doi:10.1002/dvdy.24155 pmid:24958384 pmcid:PMC4415381 fatcat:tumwmojagvghdeabpmkg7jyq4y

The mouse gene expression database: New features and how to use them effectively

Jacqueline H. Finger, Constance M. Smith, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald
2015 Genesis  
The Gene Expression Database (GXD) is an extensive and freely available community resource of mouse developmental expression data.  ...  As an integral component of the Mouse Genome Informatics (MGI) Resource, GXD combines expression data with genetic, functional, phenotypic and disease-related data, and provides tools for the research  ...  GXD thanks the GEISHA, Xenbase and ZFIN resources for their help in establishing links between our respective databases.  ... 
doi:10.1002/dvg.22864 pmid:26045019 pmcid:PMC4545717 fatcat:6kygkmdf4zh5togap5lhwvqzaq

EMAGE mouse embryo spatial gene expression database: 2014 update

Lorna Richardson, Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Julie Moss, Liz Graham, Nicholas Burton, Bill Hill, Jianguo Rao, Richard A. Baldock, Chris Armit
2013 Nucleic Acids Research  
EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression.  ...  EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns.  ...  The EMAGE database aims to fully describe gene expression patterns within the developing mouse embryo.  ... 
doi:10.1093/nar/gkt1155 pmid:24265223 pmcid:PMC3965061 fatcat:sivy6opkcrfjjofclqyirfqenq

Mouse Genome Informatics (MGI): latest news from MGD and GXD

Martin Ringwald, Joel E. Richardson, Richard M. Baldarelli, Judith A. Blake, James A. Kadin, Cynthia Smith, Carol J. Bult
2021 Mammalian Genome  
The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI's two major knowledgebases.  ...  MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information  ...  Acknowledgements We thank all the MGI curators and developers for their dedication and their many contributions to MGI. We are grateful to Dr. Hagit Shatkay (University of Delaware) and Dr.  ... 
doi:10.1007/s00335-021-09921-0 pmid:34698891 pmcid:PMC8913530 fatcat:zwlwn4gb5vhwzfnkx5qszjn7ii

Orthology for comparative genomics in the mouse genome database

Mary E. Dolan, Richard M. Baldarelli, Susan M. Bello, Li Ni, Monica S. McAndrews, Carol J. Bult, James A. Kadin, Joel E. Richardson, Martin Ringwald, Janan T. Eppig, Judith A. Blake
2015 Mammalian Genome  
The mouse genome database (MGD) is the model organism database component of the mouse genome informatics system at The Jackson Laboratory.  ...  MGD is the international data resource for the laboratory mouse and facilitates the use of mice in the study of human health and disease.  ...  Acknowledgments This work is funded through NIH grants HG000330 to MGD, HG002273 to the Gene Ontology Consortium, and HD062499 to GXD.  ... 
doi:10.1007/s00335-015-9588-5 pmid:26223881 pmcid:PMC4534493 fatcat:gsj5nwfyj5b4jkwsku72xkysve

Mouse Genome Informatics (MGI): reflecting on 25 years

Janan T. Eppig, Joel E. Richardson, James A. Kadin, Martin Ringwald, Judith A. Blake, Carol J. Bult
2015 Mammalian Genome  
From its inception in 1989, the mission of the Mouse Genome Informatics (MGI) resource remains to integrate genetic, genomic, and biological data about the laboratory mouse to facilitate the study of human  ...  This mission is ever more feasible as the revolution in genetics knowledge, the ability to sequence genomes, and the ability to specifically manipulate mammalian genomes are now at our fingertips.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s00335-015-9589-4 pmid:26238262 pmcid:PMC4534491 fatcat:uevvmlmyobagjowk5fuggyflze

Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design

Melissa D. Clarkson
2016 BMC Developmental Biology  
A total of 14 anatomical atlases and 21 gene expression resources are included.  ...  These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures  ...  GUDMAP [25] is a database of gene expression in the mouse urogenital system.  ... 
doi:10.1186/s12861-016-0116-y pmid:27206491 pmcid:PMC4875762 fatcat:cj2kfs2eyrbxtcjvcflc5yjedi

Application of comparative biology in GO functional annotation: the mouse model

Harold J. Drabkin, Karen R. Christie, Mary E. Dolan, David P. Hill, Li Ni, Dmitry Sitnikov, Judith A. Blake
2015 Mammalian Genome  
The GOC engages all contributors to work to a defined standard of curation that is presented here in the context of annotation of genes in the laboratory mouse.  ...  The Gene Ontology Consortium (GOC) consists of a large team of contributors including curation teams from most model organism database groups as well as curation teams focused on representation of data  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s00335-015-9580-0 pmid:26141960 pmcid:PMC4602061 fatcat:k47bsdddonfu5mshersdhcvgui

Leveraging Online Resources to Prioritize Candidate Genes for Functional Analyses: Using the Fetal Testis as a Test Case

Kathryn S. McClelland, Humphrey H.-C. Yao
2017 Sexual Development  
Is the gene of interest expressed in the system of interest (using expression databases)? Where else is this gene expressed (using added-value transcriptomic resources)?  ...  What pathways and processes is the gene involved in (using enriched gene pathway analysis and mouse knockout databases)?  ...  Acknowledgements We thank members of the Yao Lab for helpful discussions on the concepts in this paper.  ... 
doi:10.1159/000455113 pmid:28196369 fatcat:fw3pybkg2jertijab322dstcfa

The 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes

Michael Y. Galperin, Xosé M. Fernández-Suárez, Daniel J. Rigden
2017 Nucleic Acids Research  
As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and proteinprotein interactions.  ...  An updated version of the NAR Molecular Biology Database Collection is available at http: //www.oxfordjournals.org/nar/database/a/.  ...  Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd for their help in assembling this issue.  ... 
doi:10.1093/nar/gkw1188 pmid:28053160 pmcid:PMC5210597 fatcat:jbvd2nm6undn5k4rtwng33pxiq

VDAC Genes Expression and Regulation in Mammals

Federica Zinghirino, Xena Giada Pappalardo, Angela Messina, Giuseppe Nicosia, Vito De Pinto, Francesca Guarino
2021 Frontiers in Physiology  
RNA-seq transcriptome analysis shows that VDAC isoforms are expressed in human and mouse tissues at different levels with a predominance of VDAC1 and VDAC2 over VDAC3, with the exception of reproductive  ...  Analysis of VDAC core promoters has highlighted that, both in a human and a mouse, VDAC genes show features of TATA-less ones.  ...  The mouse Gene Expression Database (GXD): 2021 update.  ... 
doi:10.3389/fphys.2021.708695 fatcat:kiw7vgjk2rfkpe4ycz3ksbojwm

A mouse informatics platform for phenotypic and translational discovery

Natalie Ring, Terrence F. Meehan, Andrew Blake, James Brown, Chao-Kung Chen, Nathalie Conte, Armida Di Fenza, Tanja Fiegel, Neil Horner, Julius O. B. Jacobsen, Natasha Karp, Thomas Lawson (+14 others)
2015 Mammalian Genome  
The International Mouse Phenotyping Consortium (IMPC) is providing the world's first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene.  ...  Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies.  ...  Acknowledgments The Mouse Phenotyping Informatics Infrastructure is supported by the NIH Common Fund Mechanism [U54 HG006370-01] and EMBL-EBI Core Funding (to H.P.).  ... 
doi:10.1007/s00335-015-9599-2 pmid:26314589 pmcid:PMC4602054 fatcat:hspybovwnncuncfdfxkzavecje

Museum of Spatial Transcriptomics [article]

Lambda Moses, Lior Pachter
2021 biorxiv/medrxiv   pre-print
To assess the ability and potential of spatial gene expression technologies to drive biological discovery, we present a curated database of literature on spatial transcriptomics dating back to 1987, along  ...  In the past decade high-throughput technologies have been developed to quantify gene expression in space, and computational methods have been developed that leverage spatial gene expression data to identify  ...  Model organism databases collecting the proliferating gene expression patterns from various sources were also established in this period, such as gene expression database (GXD) [57] and Zebrafish Information  ... 
doi:10.1101/2021.05.11.443152 fatcat:hzue3oixczabpjwm6vwi36zila

Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse

Janan T. Eppig
2017 ILAR journal  
mouse.  ...  The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory  ...  : Disease Connection; Gene Expression Database (GXD); Recombinase (cre); Function; Strains; Strains, SNPs and Polymorphisms; Vertebrate Homology; Mouse Models of Human Cancer; Pathways; Batch Data and  ... 
doi:10.1093/ilar/ilx013 pmid:28838066 pmcid:PMC5886341 fatcat:6crth734sjb6hiutnvjqm5r764
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