ArticleG3 (Bethesda, Md.)2022
Prioritizing candidate eQTL causal genes in Arabidopsis using RANDOM FORESTS.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- Trans-QTL Alliance of HKT1 and PHL7 Modulate Salinity Stress Tolerance and Enhance Crop Yield Endurance.Plant biotechnology journal · 2026Article
- Benchmarking ensemble and deep learning models for drought-responsive gene prioritisation in rice using multi-omics data.PloS one · 2026Article
- Plasticity of maternal environment-dependent expression-QTLs of tomato seeds.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
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Authors and funding
4 authors.
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Abstract
Expression quantitative trait locus mapping has been widely used to study the genetic regulation of gene expression in Arabidopsis thaliana. As a result, a large amount of expression quantitative trait locus data has been generated for this model plant; however, only a few causal expression quantitative trait locus genes have been identified, and experimental validation is costly and laborious. A prioritization method could help speed up the identification of causal expression quantitative trait locus genes. This study extends the machine-learning-based QTG-Finder2 method for prioritizing candidate causal genes in phenotype quantitative trait loci to be used for expression quantitative trait loci by adding gene structure, protein interaction, and gene expression. Independent validation shows that the new algorithm can prioritize 16 out of 25 potential expression quantitative trait locus causal genes within the top 20% rank. Several new features are important in prioritizing causal expression quantitative trait locus genes, including the number of protein-protein interactions, unique domains, and introns. Overall, this study provides a foundation for developing computational methods to prioritize candidate expression quantitative trait locus causal genes. The prediction of all genes is available in the AraQTL workbench (https://www.bioinformatics.nl/AraQTL/) to support the identification of gene expression regulators in Arabidopsis.
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Registered trials
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