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A candidate gene is a gene, located in a chromosome region suspected of being involved in the expression of a trait such as a disease, whose protein product suggests that it could be the gene in question. A candidate gene can also be identified by association with the phenotype and by linkage analysis to a region of the genome.
A popular way to identify candidate genes is by microarray, this allows the researcher to analyse the expression levels of specific genes in a case control study, therefore if a gene is dysregulated in a disease it may be identified by microarray. However microarray has its weaknesses as it identifies all expression in the cell and could be reporting the expression of a gene which is effected by the disease rather than the cause.