U.S. Database Coordination ActivitiesSupported by Allotments of Regional Research Funds, Hatch Act For the Period 1/1/10-12/31/10January 15, 2011 | |||
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OVERVIEW:
Coordination of the CSREES National Animal Genome Research
Program's (NAGRP) Bioinformatics is primarily based at, and led from, Iowa
State University (ISU), with additional activities at Mississippi State
University (MSU) and is supported by NRSP-8. The NAGRP is made up of the
membership of the Animal Genome Technical Committee, including the
Database Subcommittee.
FACILITIES AND PERSONNEL: James Reecy, Department of Animal Science, ISU, serves as Coordinator with Susan J. Lamont (ISU), Max Rothschild (ISU), Chris Tuggle (ISU), and Shane Burgess (MSU) as Co-Coordinators. Iowa State University provides facilities and support. OBJECTIVES: The NRSP-8 project was renewed as of 10/01/08, with the following objectives: 1. Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest; 2. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes; and 3. Develop, integrate and implement bioinformatic resources to support the discovery of genetic mechanisms that underlie traits of interest. PROGRESS TOWARD OBJECTIVE 1: Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. See activities listed below. PROGRESS TOWARD OBJECTIVE 2. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. Over the past year, we have partnered with researchers at Kansas State University, Michigan State University, Iowa State University and U.S. Department of Agriculture to further develop relational databases to store and disseminate phenotypic and genotypic information from large genomic studies in farm animals. For example, we are working with the PRRS CAP Host Genome consortium to develop a relational database to house individual animal genotype and phenotype data (http://www.animalgenome.org/lunney/index.php). This will help the consortium, whose individual research labs lack expertise with relational databases, share information among consortium members and thereby facilitate data analysis. PROGRESS TOWARD OBJECTIVE 3: Develop, integrate and implement bioinformatic resources to support the discovery of genetic mechanisms that underlie traits of interest. The following describes the project's activities over this past year.
Poultry In response to a request from the NRSP8 Avian community at PAG 2009, a team lead by Parker Antin (U. Arizona), Shane Burgess and Carl Schmidt (U. Delaware) have developed a draft Avian Model Organism Database (MOD) called "Birdbase" (http://birdbase.net/).
Cattle A web site for the Ruminant Genome Biology Consortium activities is now online. It is hosted at the NAGRP Bioinformatics site and can be seen at either http://www.animalgenome.org/ruminants/ or http://www.ruminants.org/
Porcine By working with the pig genome annotation consortium groups, we have developed a pig gene WishList to facilitate the annotation activities (http://www.animalgenome.org/cgi-bin/host/ssc/gene2bacs). This website lists the BAC to which specific gene sequences have been mapped using BLAST. Several groups, primarily the Immune Response Annotation Group (IRAG) headed by Chris Tuggle and Claire Rogel-Gaillard (INRA-Jouy en-Josas), are using this website information to manually annotate gene-encoding regions on the porcine genome sequence. The IRAG group has annotated more than 1,000 regions out of a planned 1,400 total regions thought to contain immune response genes. The NAGRP blast server was updated in time for users to blast their genes of interest against the newly assembled pig genome. It has been heavily used and quite useful to the community.
Sheep
Aquaculture
Multi-species In a separate project, the Tuggle group, in collaboration with others including James Reecy, have developed a public open-source database and website (www.ANEXdb.org) for storage and analysis of functional genomics data in livestock (Couture et al. 2009). During 2010, ANEXdb was expanded beyond Affymetrix array data to include two-color array data as well. In addition, the database was migrated to NRSP-8 computer resources.
Ontology development
Software development As a result of collaborations between Iowa State University, the Medical College of Wisconsin, and University of Iowa, we are happy to release an updated version of the Virtual Comparative Map (VCMap) tool (http://bioneos.com/VCMap/). Please feel free to try things out, and send any feedback to: vcmap@bioneos.com. We have also worked with Jill Madox from Australia to set up a web site for user interactions in improving the CRIMAP software (http://www.animalgenome.org/tools/share/crimap/).
Minimal standards development
Expanded Animal QTLdb functionality
Facilitating research OBJECTIVE 1: Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest, Enhance ANEXdb.org capabilities for storage and analysis of gene expression data for all livestock species. OBJECTIVE 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. We will seek to partner with any NRSP-8 members wishing to warehouse phenotypic and genotypic data in customized relational databases. This will help consortia/researchers whose individual research labs lack expertise with relational databases to warehouse and share information. OBJECTIVE 3: Develop, integrate and implement bioinformatic resources to support the discovery of genetic mechanisms that underlie traits of interest. We will continue to work with bovine, mouse, rat, and human QTL database curators to develop minimal information for publication standards. We will also work with these same database groups to improve phenotype and measurement ontologies, which will facilitate transfer of QTL information across species. In addition, we will expand the QTL Database to house whole-genome association data, which will facilitate the identification of candidate genes for researchers seeking causal mutations. We will continue work with colleagues at USDA-ARS, as well as throughout Europe to develop a Bioinformatics Blueprint, similar to the Animal Genomics Blueprint recently published by USDA-CSREES, to help direct future livestock-oriented bioinformatic/database efforts. BirdBase was released for trial by all NRSP8 members in Jan 2010. Since this time, minor changes and additions have been made to Birdbase. Birdbase serves the avian clade rather than as a single model organism database. It can serve as an example for other NRSP-8species, especially the Aquaculture community because of the similarities in systems and species diversity. An update on the BirdBase site and results of the user survey will be presented at the 2011 PAG poultry meeting (NC1170) by Parker Antin, Shane Burgess, Fiona McCarthy and Carl Schmidt. An associated user-community survey will be analyzed by Burgess and the results presented to the NRSP8 Bioinformatics committee co-coordinators. A decision will be made at that time about whether future support/investment in BirdBase via NRSP-8 will be requested. We are working to integrate microarray element sequences with genome data for improved orthology/comparative systems biology analyses as well as the integration of expression and genome location. This work is being initiated in the pig to facilitate genome annotation but could be extended to other species using available expression profiling tools and genome sequences. Publications:
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