Identifier and database from the same sequence repository provide the greatest number of correct pairings between RNA and protein data

There is increasing interest in the integrated analysis of RNA and protein datasets to provide a more holistic description of a biological system. To do so, gene and protein identifiers can be paired by using databases that cross-link identifiers from multiple public databases. However, little is known about how using different identifiers and cross-linking databases influence the accuracy and completeness of the resulting gene-protein pairs. We investigated this by matching an existing dataset of rat proteins to their corresponding genes using different combinations of identifiers and databases from the NCBI and PIR repositories. We found that using identifier and cross-linking database from the same sequence repository yielded the most correct gene-protein pairs and consequently maximized the amount of proteins that could be compared with their gene counterparts. Overall using the GeneInfo identifier and the Entrez database, we matched 84% of the 4,016 proteins in our dataset to their corresponding genes.