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  • 18th International Mouse Genome Conference (2004)
    have always been an important resource for biological analysis Until recently polymorphisms e g RFLPs and SSLPs have been used primarily as mapping landmarks New technology for large scale detection of single nucleotide multiple nucleotide and deletion insertion polymorphisms SNPs MNPs and DIPs respectively offers the potential to correlate phenotypic differences directly to base changes in the DNA Large data sets offering dense coverage across the genome are already available as are public repositories of these data e g dbSNP MGI http www informatics jax org adds value to data by integration both within and across data domains and by offering the integrated resource for query display and download The database has always included polymorphism data e g RFLPs and SSLPs We now plan to integrate mouse SNP data and to provide interfaces that exploit this integration For example a user will be able to query for SNPs mapping within a specified bp range near genes mapped to the genome assembly sequence known to be involved in DNA repair via GO annotations where those genes occur within any QTL region for radiation induced apoptosis e g Rapop1 et al based on the MGD genetic map We will describe our plans

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file157.shtml (2016-02-17)
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  • 18th International Mouse Genome Conference (2004)
    FOR PROTEOME WIDE PROTEIN PROTEIN INTERACTION MAPS Zhong J 1 Finley R 2 1 Current affiliation Laboratory of Genetics National Institute on Aging NIH Baltimore MD United States 2 Center for Molecular Medicine and Genetics Wayne State University Detroit MI United States Most cellular activities are carried out by stable or transient protein protein interactions A proteome wide protein interaction map could suggest the functions of individual proteins help map entire pathways or processes and suggest how individual pathways and processes are integrated into larger cellular events The yeast two hybrid system is an efficient and sensitive way to detect binary protein interactions and can be modified for high throughput assays However most high throughput two hybrid approaches fail to detect many interactions that should be detected by yeast two hybrid systems and they produce a significant number of false positives We developed an alternative high throughput two hybrid approach in which two yeast arrays conditionally expressing AD or BD fusions are mated using a two phase pooled mating scheme We show that our approach allows us to detect interactions not detected by other approaches including interactions involving proteins which can activate the reporters on their own and proteins that

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file158.shtml (2016-02-17)
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  • 18th International Mouse Genome Conference (2004)
    the MGSCv3 Work is ongoing to produce a high quality finished genome using clone based sequence Currently over 50 of the mouse genome is covered by high quality finished sequence and the rest is covered by draft sequence and WGS contigs Finished sequence is hand curated and assembled into non redundant contiguous sequences contigs In an effort to provide access to the most current data we have been performing genome assemblies using all available data Whole Genome Shotgun Contigs and BAC based sequence Performing the composite assemblies has provided us with some insight concerning differences between clone based assemblies and WGA Recently we have performed several composite assemblies using different parameters on the same set of sequences In addition to producing a better mouse genome assembly we have been able to assess errors that are likely to occur when a given data source is allowed to drive the assembly Assemblies produced where clone based data drives the assembly can have local order and orientation errors when a large amount of draft sequence is included By contrast assemblies where the WGS contigs drive the assembly have an increased rate of artificial duplication This has led us to more systematically characterize the

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file159.shtml (2016-02-17)
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  • 18th International Mouse Genome Conference (2004)
    greatly A Whole Genome Shotgun WGS assembly generated by the Mouse Genome Sequencing Consortium MGSC was released and published During the past year sequencing resources for mouse have shifted towards clone based HTGS sequence As of June 4 2004 1 48 Gb of non redundant finished sequence and 1 8 Gb of redundant draft sequence were available Greater than 95 of the HTGS sequence is from the reference strain C57BL 6J To leverage all available sequence data NCBI has been performing composite assemblies that integrate HTGS sequence from C57BL 6J into the MGSCv3 NCBI Build 33 based on data from May 30 2004 integrated 1 1 Gb of HTGS phase 3 finished sequence In addition to producing the reference assembly NCBI has been producing alternate strain specific assemblies In Mouse Build 33 6 alternate assemblies were produced In addition the publicly available portion of the Celera mouse assembly Mmu16 is annotated and available as part of the standard NCBI resource set Map Viewer the NCBI ftp site Entrez Gene etc In addition to producing these assemblies NCBI provides annotation for all assemblies via a suite of software tools available from our website http www ncbi nlm nih gov Current annotation

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file160.shtml (2016-02-17)
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  • 18th International Mouse Genome Conference (2004)
    JT Sequences and Maps Group MGI Phenotypes Group MGI Expression Group MGI Software Group MGI The Jackson Laboratory Bar Harbor United States The mouse genome sequence serves as a framework for the discovery of genes that underlie biological and disease processes To leverage the genome sequence effectively depends on how well genetically defined mutant phenotypes are integrated with genome annotations and information about sequence variation e g SNPs allelic variation gene expression homology and gene function annotations Because of its long standing focus on the integration of exactly these kinds of diverse biological data about mouse genes the Mouse Genome Informatics database is a powerful platform to assist in the computational analysis of integrated biological data with the goal of identifying candidate genes associated with complex genetically defined phenotypes Associating expression phenotypes with mutant phenotypes has proved to be a powerful approach to identifying candidate genes in regions of the mouse genome to which complex traits have been mapped To facilitate such associations via MGI we have integrated probe sets from both Affymetrix and Agilent with genes in MGI As a result researchers can map expression data generated from these platforms to genes in MGI using both genomic and genetic

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file161.shtml (2016-02-17)
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  • 18th International Mouse Genome Conference (2004)
    Snoddy J GST at Oak Ridge National Lab and University of Tennessee Oak Ridge United States There are novel bioinformatics challenges posed by the study of biological systems Highly networked systems create phenotypes from genotypes and the environment We now need efforts to understand how those genes gene products and cells function in these networks This will require large data sets whose analysis will further require new bioinformatics While databases of experimental information are necessary indeed critical they are not sufficient to help obtain insight from the analysis of large complex networks We need a mathematical language to describe the interconnections of these networks i e robust tools that can help us get insights from use of that language and data mining tools to see patterns among these networks A number of both experimental and computational collaborators have been working together to develop these needed improvements Our current work involves elucidating aspects of regulatory networks and co expression networks We are integrating data from different DNA microarray data sets from gene product function data e g GO gene families genetic variation evolutionary conservation of coding and non coding parts of the genome and other similar information We are developing methods

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file162.shtml (2016-02-17)
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  • 18th International Mouse Genome Conference (2004)
    USA Plenary Presentations Oral Presentations Poster Abstracts Photos Verne Chapman Memorial Lecture Table of Contents Attendees Awards POSTER 111 THE UTILITY OF HIGH DENSITY GENETIC MAPS IN EXPERIMENTAL MOUSE CROSSES Leonardson AS Edwards SW Cervino ACL Schadt EE rosetta merck seattle United States We have examined the genetics of gene expression in an F2 mouse intercross using both a microsatellite marker map and a high density SNP marker map We

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file163.shtml (2016-02-17)
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  • 18th International Mouse Genome Conference (2004)
    SC The Jackson Laboratory Bar Harbor Maine United States The Mouse Phenome Project is an ongoing international collaborative effort to enhance the research potential of the laboratory mouse by a promoting the phenotypic and genotypic characterization of a set of 40 inbred strains and their derivatives and b making the data publicly available through a web accessible database the Mouse Phenome Database MPD www jax org phenome Grubb et al 2004 We have collected and annotated over 600 measurements that include a broad range of metabolic developmental and behavioral parameters relevant to human disease Also large volumes of SNP data are being incorporated into the MPD to maximize community SNP resources More than 450 000 SNPs have been identified by large scale genotyping consortia in a subset of the Project s 40 priority strains and contributed to the MPD Strain characteristics and genotypic data have proven to be a valuable resource for the biomedical research community as indicated by the increasing use of the MPD and significant advances using the data and associated analytical tools to uncover information on the genetic and biological factors involved in normal and disease pathways Expansion of the Mouse Phenome Project will allow the biomedical

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file164.shtml (2016-02-17)
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