title: PETModule: a motif module based approach for enhancer target gene prediction.
abstract: The identification of enhancer-target gene (ETG) pairs is vital for the understanding of gene transcriptional regulation. Experimental approaches such as Hi-C have generated valuable resources of ETG pairs. Several computational methods have also been developed to successfully predict ETG interactions. Despite these progresses, high-throughput experimental approaches are still costly and existing computational approaches are still suboptimal and not easy to apply. Here we developed a motif module based approach called PETModule that predicts ETG pairs. Tested on eight human cell types and two mouse cell types, we showed that a large number of our predictions were supported by Hi-C and/or ChIA-PET experiments. Compared with two recently developed approaches for ETG pair prediction, we shown that PETModule had a much better recall, a similar or better F1 score, and a larger area under the receiver operating characteristic curve. The PETModule tool is freely available at http://hulab.ucf.edu/research/projects/PETModule/.
authors.affiliation: Department of Electrical Engineering &Computer Science, University of Central Florida, Orlando, FL, 32816, USA.
authors.forename: Changyong
authors.initials: C
authors.lastname: Zhao
authors.affiliation: Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, 32816, USA.
authors.forename: Xiaoman
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Electrical Engineering &Computer Science, University of Central Florida, Orlando, FL, 32816, USA.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Hu
mesh_terms: D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors