Description
The Animal Quantitative Trait Loci Database (QTLdb)
collects all publicly available trait mapping data (i.e., QTL (phenotype/expression,
association data, candidate gene/GWAS) and copy number variations (CNV)) mapped
to livestock animal genomes to facilitate locating and comparing discoveries
within and between species. New data and database tools are continually
developed to align various trait mapping data to map-based genome features
such as annotated genes.
The following animals are a part of the Animal QTLdb:
Methods
The trait mapping/QTL data within the Animal QTLdb were manually curated from
published journal papers or contributed by individuals as part of the publication
process to make the data available to the public. The QTL data for collection
include phenotype/expression, association, candidate gene, GWAS, or copy number
variations (CNV). The parameters and criteria for data collection are documented
in the Curators' Manual and data quality control implemented in the
curator/editor database tools.
Credits
Zhi-Liang Hu, Carissa A. Park, Eric R. Fritz and James M. Reecy from Iowa State
University form the main development task force. Svetlana Dracheva, Wonhee Jang,
and Donna Maglott from NCBI helped with data streamlining into the GeneDB;
Xiao-Lin Wu from University of Wisconsin contributed a meta-analysis script;
and John Bastiaansen from Wageningen University and Max F. Rothschild from Iowa
State University were involved in the initial developmental work in the database's
early days. The project has been mainly supported by the USDA-NIFA NRSP-8 fund
to the NAGRP Bioinformatics Coordination team led by James Reecy at Iowa State University.
References
Hu ZL, Dracheva S, Jang W, Maglott D, Bastiaansen J, Rothschild MF, Reecy JM.
A QTL resource and comparison tool for pigs: PigQTLDB.
Mamm Genome. 2005 Oct;16(10):792-800.
PMID: 16261421
Hu ZL, Park CA, Fritz ER, and Reecy JM (2010).
QTLdb:
A Comprehensive Database Tool Building Bridges between Genotypes and Phenotypes.
Invited Lecture with full paper published electronically on The 9th World Congress on Genetics Applied to
Livestock Production. Leipzig, Germany August 1-6, 2010.
Hu ZL, Park CA, Wu XL, Reecy JM.
Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in
the post-genome era.
Nucleic Acids Res. 2013 Jan;41(Database issue):D871-9.
PMID: 23180796; PMC: PMC3531174
Hu ZL, Reecy JM.
Animal QTLdb: beyond a repository. A public platform for QTL comparisons and integration with
diverse types of structural genomic information.
Mamm Genome. 2007 Jan;18(1):1-4.
PMID: 17245610
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