How to determine the direction of regulation of a gene by comparing gene expressions? I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a specific disease. I am confused about how people can determine whether a gene is down-regulated or up-regulated by its gene expression. Assume we have a few samples of a gene: some of the samples are normal patients samples and rest of them are disease-infected samples. Do we determine the direction of regulation of a gene by the ratio of gene expression of normal/disease-infected samples? For example, if the ratio of expressions is a negative value, do we say that the gene is a down-regulated gene, otherwise, it is a up-regulated gene ?

If you have control expression values $c$ and e.g. disease expression values $d$, you take the ratio: $\frac{d}{c}$. If this is greater than one, it's up-regulated. Usually, the log-ratio is computed: $log\frac{d}{c}$. Now, if this is positive, the gene is up-regulated.

Gene expression values are usually measured genome-wide and then normalized before computing the ratios. So you rarely deal with individual raw expression values.