Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast.

ABSTRACT:

Background

Transcriptional regulation of gene expression in eukaryotes is usually accomplished by cooperative transcription factors (TFs). Computational identification of cooperative TF pairs has become a hot research topic and many algorithms have been proposed in the literature. A typical algorithm for predicting cooperative TF pairs has two steps. (Step 1) Define the targets of each TF under study. (Step 2) Design a measure for calculating the cooperativity of a TF pair based on the targets of these two TFs. While different algorithms have distinct sophisticated cooperativity measures, the targets of a TF are usually defined using ChIP-chip data. However, there is an inherent weakness in using ChIP-chip data to define the targets of a TF. ChIP-chip analysis can only identify the

SUBMITTER: Wu WS 

PROVIDER: S-EPMC4682405 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature