title: In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences.
abstract: Enhancers interact with gene promoters and form chromatin looping structures that serve important functions in various biological processes, such as the regulation of gene transcription and cell differentiation. However, enhancers are difficult to identify because they generally do not have fixed positions or consensus sequence features, and biological experiments for enhancer identification are costly in terms of labor and expense. In this work, several models were built by using various sequence-based feature sets and their combinations for enhancer prediction. The selected features derived from a recursive feature elimination method showed that the model using a combination of 141 transcription factor binding motif occurrences from 1,422 transcription factor position weight matrices achieved a favorably high prediction accuracy superior to that of other reported methods. The models demonstrated good prediction accuracy for different enhancer datasets obtained from different cell lines/tissues. In addition, prediction accuracy was further improved by integration of chromatin state features. Our method is complementary to wet-lab experimental methods and provides an additional method to identify enhancers.
authors: Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.|College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors: Yaping
authors: Y
authors: Fang
authors: Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.|College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors: Yunlong
authors: Y
authors: Wang
authors: Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.|College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors: Qin
authors: Q
authors: Zhu
authors: Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.|College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors: Jia
authors: J
authors: Wang
authors: Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.|College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.|National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors: Guoliang
authors: G
authors: Li
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D003198:Computer Simulation; D066264:Datasets as Topic; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D006657:Histones / Q000235:genetics / Q000378:metabolism; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D014157:Transcription Factors