Negative Example Aided Transcription Factor Binding Site Search

TL;DR

This paper introduces new methods for transcription factor binding site search that leverage negative examples, demonstrating improved performance over existing techniques in bacterial and eukaryotic contexts.

Contribution

The paper proposes the 2-centroid and optimal discriminating vector methods that incorporate negative examples, enhancing binding site search accuracy.

Findings

Proposed methods outperform centroid and PSSM methods.

Methods outperform a state-of-the-art approach.

Effective for both bacterial and eukaryotic transcription factors.

Abstract

Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of negative examples in binding site search is still very limited. We propose the 2-centroid and optimal discriminating vector methods, taking into account negative examples. Cross-validation results on E. coli transcription factors show that the proposed methods benefit from negative examples, outperforming the centroid and position-specific scoring matrix methods. We further show that our proposed methods perform better than a state-of-the-art method. We characterize the proposed methods in the context of the other compared methods and show that, coupled with motif subtype identification, the proposed methods can be effectively applied to a wide range of transcription factors. Finally, we argue that the proposed methods are well-suited for eukaryotic transcription factors as well. Software tools are available at: http://biogrid.engr.uconn.edu/tfbs_search/.