Evolutionary Optimization of Transcription Factor Binding Motif Detection
文献类型：期刊论文
| 作者 | Zhang Zhao; Wang Ze; Mai Guoqin; Luo Youxi; Zhao Miaomiao; Zhou Fengfeng |
| 刊名 | Advances in Experimental Medicine and Biology
 |
| 出版日期 | 2015 |
| 英文摘要 | All the cell types are under strict control of how their genes are transcribed into expressed transcripts by the temporally dynamic orchestration of the transcription factor binding activities. Given a set of known binding sites (BSs) of a given transcription factor (TF), computational TFBS screening technique represents a cost efficient and large scale strategy to complement the experimental ones. There are two major classes of computational TFBS prediction algorithms based on the tertiary and primary structures, respectively. A tertiary structure based algorithm tries to calculate the binding affinity between a query DNA fragment and the tertiary structure of the given TF. Due to the limited number of available TF tertiary structures, primary structure based TFBS prediction algorithm is a necessary complementary technique for large scale TFBS screening. This study proposes a novel evolutionary algorithm to randomly mutate the weights of different positions in the binding motif of a TF, so that the overall TFBS prediction accuracy is optimized. The comparison with the most widely used algorithm, Position Weight Matrix (PWM), suggests that our algorithm performs better or the same level in all the performance measurements, including sensitivity, specificity, accuracy and Matthews correlation coefficient. Our data also suggests that it is necessary to remove the widely used assumption of independence between motif positions. The supplementary material may be found at:http://www.healthinformaticslab.org/supp/ |
| 收录类别 | SCI |
| 原文出处 | http://link.springer.com/chapter/10.1007/978-94-017-9245-5_15 |
| 语种 | 英语 |
| 源URL | [http://ir.siat.ac.cn:8080/handle/172644/7128]  |
| 专题 | 深圳先进技术研究院_医工所 |
| 作者单位 | Advances in Experimental Medicine and Biology |
| 推荐引用方式 GB/T 7714 | Zhang Zhao,Wang Ze,Mai Guoqin,et al. Evolutionary Optimization of Transcription Factor Binding Motif Detection[J]. Advances in Experimental Medicine and Biology,2015. |
| APA | Zhang Zhao,Wang Ze,Mai Guoqin,Luo Youxi,Zhao Miaomiao,&Zhou Fengfeng.(2015).Evolutionary Optimization of Transcription Factor Binding Motif Detection.Advances in Experimental Medicine and Biology. |
| MLA | Zhang Zhao,et al."Evolutionary Optimization of Transcription Factor Binding Motif Detection".Advances in Experimental Medicine and Biology (2015). |
入库方式： OAI收割
来源：深圳先进技术研究院
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