Mouse genome informatics in a new age of biological inquiry

Bult, Carol J.; Richardson, Joel E.; Blake, Judith A.; Kadin, James A.; Ringwald, Martin; Eppig, Janan T.; Baldarelli, Richard M.; Baya, M.; Beal, Jon S.; Begley, Dale A.; Boddy, W.J.; Bradt, Dirck W.; Butler, N.E.; Chu, Teresa; Corbani, Lori E.; Corradi, John P.; Davisson, Muriel T.; Garippa, D.; Glass, L.H.; Grant, Patricia; Hill, David P.; King, Benjamin L.; Krupke, Debra M.; Lennon-Pierce, Moyha; Lutz, Cat; Maltais, Lois J.; Mani, Prita; McCright, Ingeborg J.; McKenzie, Louise; Näf, Dieter; Ormsby, J.E.; Ramachandran, Srinivasan; Reed, Deborah J.; Shaw, David R.; Szauter, Paul; Trombley, L.A.

doi:10.1109/bibe.2000.889586

Cited by 15 publications

(13 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, genome annotations for the mouse are most useful to biomedical researchers when the annotations are integrated with existing and emerging biological knowledge about their function, expression, phenotype associations and relationships to genes in other organisms (Bult et al 2000;Bult 2002). Realising the full power of the mouse as a model organism depends, in part, on making integrated genetic, genomic and phenotypic data available to the biomedical research community in ways that promote knowledge discovery.…”

Section: The Mgi Databasementioning

confidence: 99%

“…Data integration allows researchers to ask complex, contextual queries spanning different types of data and independently generated data sets (Bult et al 2000). Integrated data resources such as MGI are critical to develop the informatics capacity to address genome scale, and ultimately systems-level, research questions.…”

Section: Data Integrationmentioning

confidence: 99%

“…Bioinformatics resources and tools have been central to the rise of functional and comparative genomics. Data integration, in particular, has played a central role in the translation of vast quantities of data and information to the understanding of biological processes and systems (Bult et al 2000).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

From information to understanding: the role of model organism databases in comparative and functional genomics

Bult

2006

Animal Genetics

View full text Add to dashboard Cite

SummaryData integration is key to functional and comparative genomics because integration allows diverse data types to be evaluated in new contexts. To achieve data integration in a scalable and sensible way, semantic standards are needed, both for naming things (standardized nomenclatures, use of key words) and also for knowledge representation. The Mouse Genome Informatics database and other model organism databases help to close the gap between information and understanding of biological processes because these resources enforce well-defined nomenclature and knowledge representation standards. Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that organism-specific data are integrated, curated and accessible but also that the information is structured in such a way that comparison of biological knowledge across model organisms is facilitated.

show abstract

Section: The Mgi Databasementioning

confidence: 99%

Section: Data Integrationmentioning

confidence: 99%

See 1 more Smart Citation

From information to understanding: the role of model organism databases in comparative and functional genomics

Bult

2006

Animal Genetics

View full text Add to dashboard Cite

show abstract

“…Confusion can arise when multiple sequences for the same gene are submitted to sequence databases with different names (Bult et al 2000). This problem is lessened, however, if the query results contain sequences that are integrated with corresponding gene records in MGI and LocusLink, which provide standard nomenclature, synonyms, and cross references to other data sources.…”

mentioning

confidence: 99%

Connecting Sequence and Biology in the Laboratory Mouse

Baldarelli

Hill²,

Blake³

et al. 2003

Genome Res.

View full text Add to dashboard Cite

The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research group have generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrate these data with the ever-expanding knowledge about the roles of genes and gene products in biological processes, and how to provide useful views to the scientific community. Public resources, such as the National Center for Biotechnology Information (NCBI; http://www.ncbi.nih.gov), and model organism databases, such as the Mouse Genome Informatics database (MGI; http://www.informatics.jax.org), maintain the primary data and provide connections between sequence and biology. In this paper, we describe how the partnership of MGI and NCBI LocusLink contributes to the integration of sequence and biology, especially in the context of the large-scale genome and transcriptome data now available for the laboratory mouse. In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink.Large-scale sequencing and annotation efforts, such as the human and mouse genome sequencing initiatives (Lander et al 2001;Waterston et al. 2002), the RIKEN full-length enriched cDNA sequencing project (Kawai et al. 2001;Okazaki et al. 2002), and the Mammalian Gene Collection (MGC; Strausberg et al. 1999), have made publicly available a wealth of genomic and transcript information to support diverse research efforts related to understanding mammalian biology and disease. Now more than ever, users need easy access to integrated views of, and analysis tools for, high-quality information about mammalian genes and genomes. The challenge is to develop strategies for integrating these data with continually emerging knowledge about the function, variation, and regulation of genes and other genomic features. The collaboration between the Mouse Genome Informatics (MGI) group 8 and the National Center for Biotechnology Information's (NCBI) LocusLink and RefSeq groups (http:// www.ncbi.nih.gov/) exemplifies how coordinated efforts facilitate connectivity between sequence and biology in the mouse. The MGI resource provides highly integrated and curated views of genetic, genomic, and biological data for the laboratory mouse. LocusLink, through the Reference Sequence (RefSeq) project, connects biological information to the sequences of reference chromosomes, RNAs, and proteins. The MGI/LocusLink collaboration has its greatest impact through the mutual determination of the sequences which best define mouse genes. Once gene-to-sequence(s) connections are established, and associations to available information about the genes are made, the foundation is set for additional computation, curation, and Internet connectivity for the scientific community.

show abstract

“…Next, we tried to set up a multiplex PCR that simultaneously detects the ten transgenes in minimal reactions. Primer sequences were retrieved from public databases [3], other publications [7,9,11] or were originally designed for this study ( Table 2). The following mouse strains carrying specific transgenes were used to extract genomic DNA for the optimization of the multiplex PCR: B6.Cg-TgTn(sb-lacZ,GFP)IF2Jtak (RBRC01652) carrying neo, lacZ, pgk-neo, IRES and Gfp [14], C57BL/6-Tg(CAG-FLPe)36Ito (RBRC01834) carrying puro [13], CNR CP carrying HSVtk-neo (an unpublished strain kindly provided by Dr. T. Yagi, Osaka University), B6.129P2-Emx1 tm2(cre)Ito (RBRC01345) carrying cre [12], C57BL/6N-Tg(EIF1A-flp)66Mim (RBRC01252) carrying flp [24], FVB.129P2-Nf2 tm1Gth (RBRC01678) carrying hyg [10], and C57BL/6JJcl (CLEA Japan, Inc., Tokyo, Japan) for wild-type DNA.…”

mentioning

confidence: 99%

Simultaneous Detection of Multiple Transgenes for Genetically-Modified Mouse Strains

et al. 2009

View full text Add to dashboard Cite

Recent advances in the genetic manipulation of mice have enabled us to generate transgenic and knockout mice. However, it is not easy to maintain these genetically-modified mice with the high-quality necessary to meet both scientific and legal requirements. RIKEN BRC has collected various transgenic, knockout, and conditional knockout mice. To examine the genetic modifications in these strains quickly and thoroughly, we established a simultaneous PCR test to detect multiple transgenes. We have called this, the "KO-survey". The PCR condition was optimized to detect neo, puro, pgk-neo, lacZ, and HSVtk-neo in set I, and hyg, IRES, cre, flp, and Gfp in set II. This "KO-survey" is useful for providing users with mouse strains of the highest genetic quality and accurate information on their genetic modifications.

show abstract

Mouse genome informatics in a new age of biological inquiry

Cited by 15 publications

References 7 publications

From information to understanding: the role of model organism databases in comparative and functional genomics

From information to understanding: the role of model organism databases in comparative and functional genomics

Connecting Sequence and Biology in the Laboratory Mouse

Simultaneous Detection of Multiple Transgenes for Genetically-Modified Mouse Strains

Contact Info

Product

Resources

About