ATTED-II v11: A plant gene coexpression database using a sample balancing technique by subagging of principal components (Plant Cell Physiol)

Genes are generally expressed in concert with one another with data often represented by gene co-expression networks. Gene co-expression data may be useful in identifying genes with unknown functions and are generally utilized in exploring molecular processes occurring during normal development as well as during biological stresses. ATTED-II, is a database of plant gene coexpression data which has recently received an update with version 11. Within the database, nine plant species are represented with data originating from publicly available RNAseq and microarray studies. Using publicly available data is complicated by inherent sampling bias. ATTED-II uses principle component analysis and ensemble calculation (subagging) as methods of sample balancing to reduce difficulties in exploiting this rich source of data. The database enables users to examine coexpression networks between species which may prove beneficial for extrapolation of data from model species to plant species of interest globally. (Summary by Orla Sherwood, @orlasherwood) Plant Cell Physiol. 10.1093/pcp/pcac041)