Codon similarity data in ATTED-II ver 8.0 The gene-to-gene codon similarity data is organized in the form of tables, each named according to the Entrez Gene ID of a particular query gene. Each table encompasses three columns, specifying: the Entrez Gene ID of a corresponding gene, an MR (Mutual Rank) value (where a smaller number signifies a stronger relationship), and a Pearson correlation coefficient (where a larger number suggests a stronger association). Protein-coding sequences utilized in this study were retrieved from NCBI's RefSeq database. For each gene, a 61-dimensional vector was derived from the count of codons in the protein-coding sequence. In instances where multiple RefSeq sequences were associated with a single gene, the longest sequence was selected for the codon usage calculation. Pearson correlation coefficients (PCCs) were determined between the vectors of any two given genes. These PCCs were subsequently converted into MRs, employed as an index to evaluate the similarity in codon usage between the genes.

{"references": ["Aoki Y, Okamura Y, Tadaka S, Kinoshita K, Obayashi T. (2016) ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression. Plant Cell Physiology, 57, e5."]}