Data · dataset · 2014
Two-stage genome-wide search for epistasis with implementation to Recombinant Inbred Lines (RIL) populations
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Gene expression data (filter.genes.csv): Gene expression Arabidopsis thaliana data was downloaded from the TAIR database website (ftp://ftp.arabidopsis.org/home/tair/Microarrays/analyzed_data/affy_data_1436_10132005.zip).
Description
A sample of 211 RIL population individuals derived from a cross between two inbred accessions, Bayreuth-0 (Bay-0) and Shahdara (Sha), was used. Transcript (mRNA) levels were quantified using Affymetrix whole-genome microarrays with two replications (arrays) for each individual.
The gene expression data was preprocessed by the Variance Stabilization Normalization method [31]. Traits with essentially no expression (15,566 traits) were filtered out by the EM algorithm for a mixture of univariate normal distributions (using the ‘mixtools’ R package), leaving 7244 traits for the analysis. Genetic map (genetic_map.csv): The Arabidopsis Thaliana genetic map consists of 579 molecular markers.
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It was originally obtained from elp.ucdavis.edu/data/analysis/211_RILs_SFP_map/ 211_RILs_SFP_map.html. The genotypic data was preprocessed using the MultiPoint software (multiqtl.com) for the purpose of eliminating non-informative overlapping markers and those markers that cause local neighborhood instability in the map [30]. In total, 493 markers remained for the analysis.
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Where it is published
- Repository landing page figshare.com/articles/dataset/Genetic_map/1252043 ↗
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- DOI doi.org/10.6084/m9.figshare.1252043 ↗
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Documentation and papers
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Topics
- Stated by source
- Computer and information sciences
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| DataCite | 10.6084/m9.figshare.1252043 | 13 d ago | JSON v1 |
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