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The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse

A. S. Nord
2006 Nucleic Acids Research  
The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap  ...  A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains.  ...  We thank Carol Bult at Mouse Genome Informatics, Deanna Church at the National Center for Biotechnology Information, and Bob Kuhn at University of California at Santa Cruz for their helpful suggestions  ... 
doi:10.1093/nar/gkj097 pmid:16381950 pmcid:PMC1347459 fatcat:os7arloebjcshlmdhcfgryejru

The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

M. Ringwald, V. Iyer, J. C. Mason, K. R. Stone, H. D. Tadepally, J. A. Kadin, C. J. Bult, J. T. Eppig, D. J. Oakley, S. Briois, E. Stupka, V. Maselli (+6 others)
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS We would like to thank all our colleagues from the different IKMC programs for making their data available to the IKMC web portal project and for very collegial and productive interactions  ...  Finally, we would like to thank UCSC and Ensembl for displaying IKMC allele tracks on their genome browsers, and all external resources that provide data to the IKMC web portal.  ...  (12) , genes trapped by the IGTC (International Gene Trap Consortium) (13) or by TIGM, genes for which mutants are reported in MGI, and genes for which mutant ES cells or mice are available through the  ... 
doi:10.1093/nar/gkq879 pmid:20929875 pmcid:PMC3013768 fatcat:qrhhuo6nxrhgdkfqrdqsoegxwe

BioMart as an integration solution for the International Knockout Mouse Consortium

D. J. Oakley, V. Iyer, W. C. Skarnes, D. Smedley
2011 Database: The Journal of Biological Databases and Curation  
Acknowledgements We are most grateful to all the members of the IKMC programs for making the data available for creation of the BioMart datasets. In particular, we thank Jeremy C.  ...  Mason, Kevin Stone, James A. Kadin, Janan T. Eppig  ...  To date, the IKMC has produced mutant ES cell lines for 16 031 genes out of the predicted 25 000 protein coding genes in C57BL/6N ES cells.  ... 
doi:10.1093/database/bar028 pmid:21930503 pmcid:PMC3263594 fatcat:aysiqciu6vetrht6hqqxjlf5pe

EMMA--mouse mutant resources for the international scientific community

P. Wilkinson, J. Sengerova, R. Matteoni, C.-K. Chen, G. Soulat, A. Ureta-Vidal, S. Fessele, M. Hagn, M. Massimi, K. Pickford, R. H. Butler, S. Marschall (+14 others)
2009 Nucleic Acids Research  
High throughput strategies by the International Knockout Mouse Consortium (IKMC) are producing mutants for all protein coding genes.  ...  The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website.  ...  ACKNOWLEDGEMENTS The authors would like to thank the members of the EMMA Technical Working Group, Board of  ... 
doi:10.1093/nar/gkp799 pmid:19783817 pmcid:PMC2808872 fatcat:o66qke2t6vbb7bk6h5za27xpfm

The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones

G. Roma, M. Sardiello, G. Cobellis, P. Cruz, G. Lago, R. Sanges, E. Stupka
2007 Nucleic Acids Research  
Among the trapped genes, 7 728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases.  ...  The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content.  ...  Funding to pay the Open  ... 
doi:10.1093/nar/gkm825 pmid:17942430 pmcid:PMC2238955 fatcat:3lposw7ifbfg7kmbocj6p5zizq

Page 17 of None Vol. 54, Issue 3 [page]

2006 None  
Seibler J, Kuter-Luks B, Kern H, Streu S, Plum L, Mauer J, Kuhn R, portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res 34: D642-D648, 2006.  ...  Invited Review E438 MOUSE MODELS IN ENDOCRINE RESEARCH and Ferrin TE. The International Gene Trap Consortium Website: a 42.  ... 

CreZOO--the European virtual repository of Cre and other targeted conditional driver strains

C. Chandras, M. Zouberakis, E. Salimova, D. Smedley, N. Rosenthal, V. Aidinis
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We would like to thank CREATE partners for their valuable input and constructive criticism.  ...  The Cre8 portal, created in the context of the CREATE consortium, aims to integrate information from European and International Cre driver strains, through a virtual international application of genetically  ...  of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells, the majority of which are designed as conditional, activated only in specific tissue (special control) and/or life stage  ... 
doi:10.1093/database/bas029 pmid:22730454 pmcid:PMC3381224 fatcat:lla4b2rd4fdurjb7asvb5qzghm

Mouse genetic and phenotypic resources for human genetics

Paul N. Schofield, Robert Hoehndorf, Georgios V. Gkoutos
2012 Human Mutation  
We discuss the nature and availability of data, mice and ES cells from these large-scale programmes, the use of these resources to help prioritise and validate candidate genes in human genetic association  ...  Large-scale community projects using mice, based on forward and reverse genetics, and now the pan-genomic phenotyping efforts of the International Mouse Phenotyping Consortium (IMPC), are generating resources  ...  Acknowledgments The authors would like to thank Prof. Klaus Schughart and Prof. Steve Brown for helpful comments on the manuscript.  ... 
doi:10.1002/humu.22077 pmid:22422677 pmcid:PMC3473354 fatcat:izb7ubfajjcmzjteprtcmnlw24

Modeling Genetic Susceptibility to Disease ☆ [chapter]

A.C. Veith, C. Chu, B. Moorthy
2018 Comprehensive Toxicology  
The KOMP is currently working to mutate all protein-encoding genes in the mouse and make them available to investigators while the International Mouse Phenotyping Consortium (IMPC) is working to provide  ...  Many previously generated gene trap vectors have been generated by the International Gene Trap Consortium and are available at the Mutant Mouse Resource and Research Centers (MMRRC).  ... 
doi:10.1016/b978-0-12-801238-3.95609-5 fatcat:rw3b4lzxvfhztm6voh7epgtn7m

BioMart – biological queries made easy

Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk
2009 BMC Genomics  
In this paper, we describe all aspects of BioMart from a user's perspective and demonstrate how it can be used to solve real biological use cases such as SNP selection for candidate gene screening or annotation  ...  This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution.  ...  At the Ontario Institute for Cancer Research work funding is provided by the government of Ontario. We are most grateful to Cara Woodwark for her feedback on this manuscript.  ... 
doi:10.1186/1471-2164-10-22 pmid:19144180 pmcid:PMC2649164 fatcat:cn2znm3jdjbfrimhmkgulgfjbe

Molecular neuroanatomy: a generation of progress

Jonathan D. Pollock, Da-Yu Wu, John S. Satterlee
2014 Trends in Neurosciences  
We also thank Dr Christina Liu for helpful discussions in preparation of this manuscript.  ...  Acknowledgments J.D.P. wishes to thank Drs Anthony Zador and Ed Boyden for helpful discussions regarding neuronal barcoding.  ...  they require for their research http://www.rrrc.us/ Resources for knockout mice International Gene Trap Consortium (IGTC) IGTC represents all publicly available gene-trap cell lines, which are  ... 
doi:10.1016/j.tins.2013.11.001 pmid:24388609 pmcid:PMC3946666 fatcat:bic7nwic3neujkgrnsinidkzra

HUPHO: the human phosphatase portal

S Liberti, A Calderone, F Sacco, L Perfetto, M Iannuccelli, S Panni, E Santonico, A Palma, AP Nardozza, L Castagnoli, G Cesareni
2012 EMBnet journal  
To this end we developed a search engine to recover and integrate information annotated in several publicly available web resources.  ...  Phosphatases and kinases contribute to the regulation of protein phosphorylation homeostasis in the cell.  ...  Acknowledgement This work was supported by Telethon (GGP09243), the Italian Association for Cancer Research (AIRC), the FIRB project Oncodiet and the FP7 projects Affinomics and PSIMEX.  ... 
doi:10.14806/ej.18.a.380 fatcat:gvf4j6ktezcnnaxzvqnzmdbjn4

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

Cynthia L. Smith, Janan T. Eppig
2012 Mammalian Genome  
Finally we discuss future application of the MP in providing standard descriptors of the phenotype pipeline test results from the International Mouse Phenotype Consortium projects.  ...  A wealth of phenotype data on mouse mutations and variants annotated to the MP already exists in the Mouse Genome Informatics database.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s)  ... 
doi:10.1007/s00335-012-9421-3 pmid:22961259 pmcid:PMC3463787 fatcat:ygcz5rtafnbo7a7exo764r5vsu

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  
We discuss the publicly available online resources that can be used to answer a range of questions about a gene.  ...  We cross-referenced these genes to existing microarray data and narrowed the list down to cell-type-specific candidates (35 for Sertoli cells, 11 for Leydig cells, and 25 for germ cells).  ...  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

Brain transcriptome databases: a user's guide

Jason M. Keil, Adel Qalieh, Kenneth Y. Kwan
2018 Journal of Neuroscience  
Spatiotemporal and cell type-specific analyses of the transcriptome, the sum total of all RNA transcripts in a cell or an organ, can provide insights into the role of genes in brain development and function  ...  In the previous decade, advances in sequencing technology and funding from the National Institutes of Health and private foundations for large-scale genomics projects have led to a growing collection of  ...  The transcriptome data and the developmental trajectories of genes and pathways are publicly available in a user-friendly format from HB Atlas at http://hbatlas.org/, where individual genes can be queried  ... 
doi:10.1523/jneurosci.1930-17.2018 pmid:29437890 fatcat:wepidowg3nbt3kldoiqn2tmuka
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