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Table 1 Measures of gene expression in ascending order of complexity

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 = 1 n 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 i , j = C o v i , j σ i σ 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 i , j r B i , j 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 C d E i , j = r d E i , d E j 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