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  Matapax: An Online High-Throughput Genome-Wide Association Study Pipeline

Childs, L. H., Lisec, J., & Walther, D. (2012). Matapax: An Online High-Throughput Genome-Wide Association Study Pipeline. Plant Physiology, 158(4), 1534-1541. doi:10.1104/pp.112.194027.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-201E-D Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-201F-B
Genre: Journal Article

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 Creators:
Childs, L. H.1, Author
Lisec, J.2, Author              
Walther, D.3, Author              
Affiliations:
1External Organizations, ou_persistent22              
2Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              
3BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              

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Free keywords: arabidopsis-thaliana samples
 Abstract: High-throughput sequencing and genotyping methods are dramatically increasing the number of observable genetic intraspecies differences that can be exploited as genetic markers. In addition, automated phenotyping platforms and "omics" profiling technologies further enlarge the set of quantifiable macroscopic and molecular traits at an ever-increasing pace. Combined, both lines of technological advances create unparalleled opportunities to identify candidate gene regions and, ideally, even single genes responsible for observed variations in a particular trait via association studies. However, as of yet, this new potential is not sufficiently matched by enabling software solutions to easily exploit this wealth of genotype/phenotype information. We have developed Matapax, a Web-based platform to address this need. Initially, we built the infrastructure to support association studies in Arabidopsis (Arabidopsis thaliana) based on several genotyping efforts covering up to 1,375 Arabidopsis accessions. Based on the user-supplied trait information, associated single-nucleotide polymorphism markers and single-nucleotide polymorphism-harboring or -neighboring genes are identified using both the GAPIT and EMMA libraries developed for R. Additional interrogation is facilitated by displaying candidate regions and genes in a genome browser and by providing relevant annotation information. In the future, we plan to broaden the scope of organisms to other plant species as more genotype/phenotype information becomes available. Matapax is freely available at http://matapax.mpimp-golm.mpg.de and can be accessed using any internet browser.

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Language(s): eng - English
 Dates: 2012-02-232012
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000303001400005
DOI: 10.1104/pp.112.194027
ISSN: 1532-2548 (Electronic) 0032-0889 (Linking)
URI: ://000303001400005 http://www.plantphysiol.org/content/158/4/1534.full.pdf
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Title: Plant Physiology
Source Genre: Journal
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Pages: - Volume / Issue: 158 (4) Sequence Number: - Start / End Page: 1534 - 1541 Identifier: -