Highlighted article: J. Lloyd and D. Meinke (2012) A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis thaliana. Plant Physiology, January 2012 pp.111.192393.
In plant science, many published papers involve at least one loss-of-function mutant. A huge number of mutant Arabidopsis lines exist in labs all around the world, detailed in as many journal articles. Now however the genotype and phenotype information for loss-of-function Arabidopsis mutants is stored one place: a dataset assembled by Johnny Lloyd and David Meinke of Oklahoma State University.
Lloyd and Meinke painstakingly went through TAIR, their own database SeedGenes.org, and PubMed to find 2400 Arabidopsis thaliana genes with a loss-of-function mutant phenotype. Out of necessity, the database excludes the effects of under- or over- expression of genes.
The phenotypic effects of gene knock-outs were classified into four groups: essential, morphological, cellular-biochemical, and conditional. The groups were divided into classes reflecting the developmental stage or organ where the phenotype manifests itself, and further divided into subsets which specify the characteristic affected by the phenotype, for example ‘pigmentation’, ‘gamerophyte defective’, and ‘stomata, trichomes’.
The dataset is found in the supplementary data of the paper. Supplemental Table 2 is the complete dataset. On tab 1 the dataset is sorted by locus number and includes 19 columns of information on the gene and the mutant phenotype. This information encompasses the classification of the phenotype, a description of the phenotype, and a reference to the lab in which the research was carried out. Tab 2 is a table visualising the phenotype subsets affected by the gene mutations, and allows genes to be sorted by phenotype.
Supplemental Table 1 sets out the classification system used.
Supplemental Table 4 is the subset of mitochondrial localised proteins.
Supplemental Table 5 is a list of 155 unique genes which are not in the main dataset but encode a protein that interacts with the product of a unique gene in the dataset.
Supplemental Table 6 is a table of 591 genes associated with multiple mutant phenotypes. Four tabs detail ‘clusters’ of genes with multiple effects on phenotype.
Supplemental Table 7 matches 82 Arabidopsis genes from the main dataset with orthologs causing a similar phenotype in maize, rice, or tomato.