Prediction of TF-binding site by inclusion of higher order position dependencies

Zhou, Jiyun, Lu, Qin, Xu, Ruifeng, Gui, Lin and Wang, Hongpeng (2019). Prediction of TF-binding site by inclusion of higher order position dependencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics ,

Abstract

Most proposed methods for TF-binding site (TFBS) predictions only use low order dependencies for predictions due to the lack of efficient methods to extract higher order dependencies. In this work, We first propose a novel method to extract higher order dependencies by applying CNN on histone modification features. We then propose a novel TFBS prediction method, referred to as CNN_TF, by incorporating low order and higher order dependencies. CNN_TF is first evaluated on 13 TFs in the mES cell. Results show that using higher order dependencies outperforms low order dependencies significantly on 11 TFs. This indicates that higher order dependencies are indeed more effective for TFBS predictions than low order dependencies. Further experiments show that using both low order dependencies and higher order dependencies improves performance significantly on 12 TFs, indicating the two dependency types are complementary. To evaluate the influence of cell-types on prediction performances, CNN_TF was applied to five TFs in five cell-types of humans. Even though low order dependencies and higher order dependencies show different contributions in different cell-types, they are always complementary in predictions. When comparing to several state-of-the-art methods, CNN_TF outperforms them by at least 5.3% in AUPR.

Publication DOI: https://doi.org/10.1109/TCBB.2019.2892124
Divisions: Engineering & Applied Sciences
Additional Information: © 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Full Text Link:
Related URLs: https://ieeexpl ... authors#authors (Publisher URL)
Published Online Date: 2019-01-10
Authors: Zhou, Jiyun
Lu, Qin
Xu, Ruifeng
Gui, Lin
Wang, Hongpeng

Download

[img]

Version: Accepted Version

| Preview

Export / Share Citation


Statistics

Additional statistics for this record