Page 2 - B.Bioinformatics and systems biology

[B. Bioinformatics and systems biology-2]

Integrating binding and expression data to predict

transcription factors combined function

Mahmoud Ahmed¹, Deok Ryong Kim¹

¹Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea

Transcription factor binding on the regulatory region of a gene induces or represses its expression. Transcription
factors share their binding sites with other factors, co-factors and/or DNA-binding proteins. These proteins form
complexes which bind to the DNA as one-units. Finding protein overlapping binding sites is rarely enough to infer

a functional interaction. We propose a method to predict the combined functions of two factors using comparable

binding and expression data. The method is based on a previously suggested algorithm, which we re-implemented
in R and extended for this purpose. The output of this method is the rank of the factor's targets by importance and
a prediction of the dominant kind of interaction between two transcription factors. We applied the method on

simulated and real datasets of transcription factor-binding sites and gene expression under perturbation of factors.
We found that Yin Yang 1 transcription factor (YY1) and YY2 has antagonistic and independent regulatory targets

in HeLa cells, but they may cooperate on a small number of shared targets. We developed an R package and a web
application to apply the method of integrating binding and expression data to determine the cooperative or

competitive combined function.