Table 1

Measures of gene expression in ascending order of complexity
Measure Algebra formulae Description Example in skeletal muscle context
Expression <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/356/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/356/mathml/M1">View MathML</a> 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 <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/356/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/356/mathml/M2">View MathML</a> 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 <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/356/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/356/mathml/M3">View MathML</a> 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 <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/356/mathml/M4','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/356/mathml/M4">View MathML</a> 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 <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/356/mathml/M5','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/356/mathml/M5">View MathML</a> 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

Hudson et al.

Hudson et al. BMC Genomics 2012 13:356   doi:10.1186/1471-2164-13-356

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