DEGs and down-regulated DEGs can be visualised in terms of

gical significance. For instance, the genes above two were up-

DEGs and the genes below negative two were down-regulated

rom this plot, it can be seen that the mean expression variable has

distribution though the majority of genes have small mean

ns. The other phenomenon from this plot is that the discovered

ve a wide range distribution of the mean expressions. This means

EG may have a smaller mean expression or may have a greater

pression. One major limitation of this MA plot is that it does not

he use of the statistical significance. Therefore, in addition to the

ion of the relationship between the differential expression

and the mean expression variable, it may not be efficient to show

he discovered DEGs have the statistical significance.

MA plot generated for the prostate cancer diagnosis data, where M stands for

tial expression variable and A stands for the mean expression variable.

e visualisation of the discovered DEGs using the volcano plot

mentioned, the biological significance measurement can indicate

a gene is up- or down-regulated while the statistical significance

ment can assess the significance of the differential expression

two conditions. Combining both, therefore, can lead to

ful conclusion for a gene expression pattern discovery project.

opularly used approach to visualise the discovered DEGs for both

l significance and statistical significancy is the volcano plot [Cui

chill, 2003]. It has been widely used in gene expression pattern