Table 1.

Measures of gene expression in ascending order of complexity

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 xi,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