Animal QTLdb statistics

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Protocols

Animal QTLdb specifications

Information


Unique identifier OMICS_04527
Name Animal QTLdb
Alternative name Animal Quantitative Trait Loci database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse, Application programming interface
User data submission Allowed
Version 33.0
Maintained Yes

Maintainers


  • person_outline Zhi-Liang Hu
  • person_outline James Reecy

Publications for Animal Quantitative Trait Loci database

Animal QTLdb citations

 (9)
library_books

Genetical genomics of growth in a chicken model

2018
BMC Genomics
PMCID: 5782384
PMID: 29361907
DOI: 10.1186/s12864-018-4441-3

[…] vals were based on a 1.8 logarithm of odds (LOD) drop []. We compared the QTL with previously published growth loci from the F2 generation of the intercross, using the estimated physical locations in Animal QTLdb []. Epistatic interactions were also assessed using permutation thresholds generated using R/qtl, with a 20% suggestive and 5% significant genome-wide threshold again used. In the case of […]

call_split

Identification of copy number variation in French dairy and beef breeds using next generation sequencing

2017
PMCID: 5655909
PMID: 29065859
DOI: 10.1186/s12711-017-0352-z
call_split See protocol

[…] es were downloaded. For each gene that was located within a CNVR or overlapping with a CNVR, we used Ensembl information to verify whether there were known paralogous genes.Second, we used the public animal QTLdb database, release 32 [], to check whether the variants included in our panel were located within or overlapped with publicly available bovine quantitative trait loci (QTL).Finally, gene o […]

library_books

Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition

2017
PLoS One
PMCID: 5587268
PMID: 28877211
DOI: 10.1371/journal.pone.0184120

[…] Pig QTL data were downloaded from Animal QTLdb release 29 []. A total of 1,672 unique trait locations were selected with the class names “meat and carcass” and “production,” labeled “significant,” and with a P<0.05. The coding sequenc […]

library_books

Genome wide detection of copy number variation in Chinese indigenous sheep using an ovine high density 600 K SNP array

2017
Sci Rep
PMCID: 5430420
PMID: 28424525
DOI: 10.1038/s41598-017-00847-9

[…] ived growth factor alpha), that were previously reported to overlap with CNVs in fat-tailed sheep. We found a total of 1,094 CNVRs (84.4%) that overlap with at least one base with QTLs from the sheep Animal QTLdb (Fig.  and Additional file: Table ). Most cases proved to be CNVRs residing in a QTL region. […]

library_books

Genomic Footprints in Selected and Unselected Beef Cattle Breeds in South Korea

2016
PLoS One
PMCID: 4811422
PMID: 27023061
DOI: 10.1371/journal.pone.0151324

[…] e functions/roles of genes in the candidate regions, we used the medScan database that provides sentences from MEDLINE abstracts []. QTL regions were identified from information on Cattle QTLs in the Animal QTLdb (Release 17; http://www.animalgenome.org/cgi-bin/QTLdb/BT/index). QTL locations by bp (Btau4.0) were downloaded and meat and production trait associated QTLs were selected. The associated […]

library_books

Comparative Analyses of QTLs Influencing Obesity and Metabolic Phenotypes in Pigs and Humans

2015
PLoS One
PMCID: 4562524
PMID: 26348622
DOI: 10.1371/journal.pone.0137356

[…] with human phenotypes that were comparable to the porcine phenotypes. Data on 12,618 pig QTLs from 461 publication representing 656 different traits were also downloaded from the Animal QTL database (Animal QTLdb) [] and subsequently used to identify previously identified porcine QTLs up to 3 Mb in size that overlapped QTL regions identified in this study. These overlapping QTLs were manually cura […]

Citations

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Animal QTLdb institution(s)
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA, USA; Department of Meat and Animal Science, College of Agriculture and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA
Animal QTLdb funding source(s)
Supported by the USDA NRSP-8 National Animal Genome Research Program, Bioinformatics Coordination Project and partly by the USDA-NRI [2007-04187].

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