Pig QTL Track Settings
 
Pig Quantitative Trait Loci from animalQTLdb   (All Mapping and Sequencing tracks)

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Data last updated at UCSC: 2014-06-11

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