Table 1 Measures of gene expression in ascending order of complexity

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

$C_{i,j}=r_A\left(i,j\right)=\frac{Cov\left(i,j\right)}{{\sigma }_i{\sigma }_j}$

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

$Cd{E}_{i,j}=r\left(d{E}_i\text{,}d{E}_j\right)$

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