ase two logarithm fold change is defined as below,

ଶ^൫ܨ௚^൯ൌlogଶ^ቆߤ௚,஺

ߤ௚,஻

ቇൌlogଶ൫ߤ௚,஺൯െlogଶ൫ߤ௚,஻൯

(6.2)

a fold change is two, the base two logarithm fold change is one,

that the case mean expression is the double of the control mean

n. When a fold change is half, the base two logarithm fold change

ve one, meaning that the control mean expression is the double of

mean expression. For short, the base two logarithm fold change is

d as the fold change in the following discussions. A gene with a

fold change is called a down-regulated gene and a gene with a

fold change is called an up-regulated gene. The gene regulation

is from a control condition to a case condition. If the fold change

n-regulated gene is less than a pre-defined negative threshold, the

named as a down-regulated DEG. If the fold change of an up-

gene is greater than a pre-defined positive threshold, the gene is

an up-regulated DEG.

e 6.1 shows the distribution of the fold changes of all genes in a

ay gene expression data, in which the letrozole drug was used to

breast cancer patients [Miller, et al., 2007; Miller, et al., 2010].

set is composed of two conditions, i.e., before and after using the

e condition population was named as baseline before using the

e case population was named as letrozole after using the drug. If

change threshold was one, 22 down-regulated DEGs and six up-

DEGs were identified. All the down-regulated DEGs were on

side of the estimated density function of the fold change.

le, all the up-regulated DEGs were on the right side of the

d density function of the fold change.

ver, the fold change may have little information regarding the

significance. For instance, it has no statistical basis to compare

with a fold change 2.5 with a gene with a fold change 2.1.

e, the statistical significance is missing in the fold change space.