Sequence signatures extracted from proximal promoters can be used to predict distal enhancers.

ABSTRACT:

Background

Gene expression is controlled by proximal promoters and distal regulatory elements such as enhancers. While the activity of some promoters can be invariant across tissues, enhancers tend to be highly tissue-specific.

Results

We compiled sets of tissue-specific promoters based on gene expression profiles of 79 human tissues and cell types. Putative transcription factor binding sites within each set of sequences were used to train a support vector machine classifier capable of distinguishing tissue-specific promoters from control sequences. We obtained reliable classifiers for 92% of the tissues, with an area under the receiver operating characteristic curve between 60% (for subthalamic nucleus promoters) and 98% (for heart promoters). We next used these classifiers

SUBMITTER: Taher L 

PROVIDER: S-EPMC3983659 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature