As a result of the capacity of transposon mutagenesis to incorporate genes into most areas of target chromosomes, there are a number of functions associated with the process.
* Virulence genes in viruses and bacteria can be discovered by disrupting genes and observing for a change in phenotype. This has importance in antibiotic production and disease control.
* Non-essential genes can be discovered by inducing transposon mutagenesis in an organism. The transformed genes can then be identified by performing PCR on the organism's recovered genome using an ORF-specific primer and a transposon-specific primer. Since transposons can incorporate themselves into non-coding regions of DNA, the ORF-specific primer ensures that the transposon interrupted a gene. Because the organism survived after homologous integration, the interrupted gene was clearly non-essential.
* Cancer-causing genes can be identified by genome-wide mutagenesis and screening of mutants containing tumours. Based on the mechanism and results of the mutation, cancer-causing genes can be identified as oncogenes or tumour-suppressor genes.