Given that many biological questions are often asked to compare the difference between two different conditions, it is important to develop new programs that address the comparison of two biological ChIP-seq samples.
The detection of DE genes can lead to a better understanding of genetic and biological differences between two different conditions and to the detection of predictive biomarkers [ 51, 52].
Of the GO_slim terms associated with significant changes in expression with growth rate, none appears to show a qualitative difference between two different conditions (that is, increasing with growth rate in one while decreasing in another).
For calculations of the differences in TF T-values between two different conditions (X-Y), the following rules were set up: If the T-values of the TF has the same sign in both conditions, then purple (positive numbers) indicates a higher absolute value in YPD germination compared to glucose germination/stationary phase exit, and green vice versa (negative numbers).
While these plots show the absolute characteristics nicely, the difference between control and treatment or between two different conditions, which is usually the question of interest, is only indirectly represented.
To calculate the relative activities of miRNAs, we examine the expression changes of all genes between two different conditions measured by microarray experiments, which is denoted as "expression change profile" in this article.
Thus, the purpose of our method is to infer the relative miRNA activities, i.e. changes of miRNA effective regulations between two different conditions, based on the expression changes of their target genes, which are directly measured by cDNA arrays or calculated by comparing the absolute gene expression levels from different oligonucleotide arrays.
