From: Beyond differential expression: the quest for causal mutations and effector molecules
Measure | Algebra formulae | Description | Example in skeletal muscle context |
---|---|---|---|
Expression | ${E}_{i,A}=\frac{1}{n}\sum _{k=1}^{n}{x}_{i,k}$ | Average (normalized) expression of the i-th gene across the n samples (eg. biological replicates) of experimental condition A and where each x_{ i,k } corresponds to the expression of the i-th gene in the k-th sample (k = 1, …, n). | MYL2 is abundant, MSTN is intermediate |
Differential Expression | $d{E}_{i}={E}_{i,A}-{E}_{i,B}$ | Difference in the expression of the i-th gene in the two conditions under scrutiny, A and B (eg. healthy and diseased, two breeds, two diets, two time points, …). Note that it is not a requirement to have the same number of samples surveyed in the two conditions. | MYL2 relatively strongly, definitely not MSTN |
Co-Expression | ${C}_{i,j}={r}_{A}\left(i,j\right)=\frac{Cov\left(i,j\right)}{{\sigma}_{i}\phantom{\rule{0.12em}{0ex}}{\sigma}_{j}}\phantom{\rule{0.5em}{0ex}}$ | Similarity of expression profile (typically and shown here the Spearman correlation coefficient) between the i-th and the j-th genes across the n samples of condition A. | MYOD1 and MYOG |
Differential Co- Expression | $d{C}_{i,j}={r}_{A}\left(i,j\right)-{r}_{B}\left(i,j\right)$ | Difference in the co-expression between the i-th and the j-th genes in the two conditions under scrutiny, A and B. Note that it is not a requirement to have the same number of samples surveyed in the two conditions. | MSTN and MYL2 |
Co-Differential Expression | $Cd{E}_{i,j}=r\left(d{E}_{i}\phantom{\rule{0.1em}{0ex}}\text{,}\phantom{\rule{0.1em}{0ex}}d{E}_{j}\right)$ | Similarity of the profile of differential expression of genes i and j across the levels of another experimental design effect such as time points. Two conditions, A and B, are being surveyed across a series of developmental time points. | MYL2 and MYL3 |