title: AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana.
abstract: Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations has enabled investigation of the genetic architecture of variation in gene expression. This has the potential to enrich our understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. A number of genetical genomics studies have been published for Arabidopsis thaliana, uncovering many expression quantitative trait loci (eQTLs). However, these complex data are not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this problem with AraQTL (http://www.bioinformatics.nl/Ara QTL/), an easily accessible workbench and database for comparative analysis and meta-analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re-using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local eQTLs that could harbour candidate genes for phenotypic QTLs, or detect gene-by-environment interactions by comparing eQTLs under different conditions.
authors.affiliation: Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.|Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Harm
authors.identifier: http://orcid.org/0000-0002-9167-4945
authors.initials: H
authors.lastname: Nijveen
authors.affiliation: Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Wilco
authors.identifier: http://orcid.org/0000-0002-0228-169X
authors.initials: W
authors.lastname: Ligterink
authors.affiliation: Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Joost J B
authors.identifier: http://orcid.org/0000-0001-8918-0711
authors.initials: JJ
authors.lastname: Keurentjes
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France.
authors.forename: Olivier
authors.identifier: http://orcid.org/0000-0003-3717-0137
authors.initials: O
authors.lastname: Loudet
authors.affiliation: Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.|Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Jiao
authors.initials: J
authors.lastname: Long
authors.affiliation: Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Mark G
authors.identifier: http://orcid.org/0000-0001-7119-6213
authors.initials: MG
authors.lastname: Sterken
authors.affiliation: Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
authors.forename: Pjotr
authors.identifier: http://orcid.org/0000-0001-7119-6213
authors.initials: P
authors.lastname: Prins
authors.affiliation: Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Henk W
authors.identifier: http://orcid.org/0000-0002-6743-583X
authors.initials: HW
authors.lastname: Hilhorst
authors.affiliation: Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Dick
authors.identifier: http://orcid.org/0000-0002-4944-4310
authors.initials: D
authors.lastname: de Ridder
authors.affiliation: Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Jan E
authors.initials: JE
authors.lastname: Kammenga
authors.affiliation: Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands.
authors.forename: Basten L
authors.initials: BL
authors.lastname: Snoek
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D049490:Systems Biology; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins
keywords: 
  Arabidopsis thaliana
  ; co-expression; expression quantitative trait loci; gene expression; genetical genomics; system genetics; transcriptional regulation