An approach to predict transcription factor dna binding site specificity based upon gene and transcription factor functional categorization
文献类型：期刊论文
| 作者 | Qian, Ziliang; Lu, Lingyi; Liu, XiaoJun; Cai, Yu-Dong; Li, Yixue |
| 刊名 | Bioinformatics
 |
| 出版日期 | 2007-09-15 |
| 卷号 | 23期号:18页码:2449-2454 |
| ISSN号 | 1367-4803 |
| DOI | 10.1093/bioinformatics/btm348 |
| 通讯作者 | Cai, yu-dong(cyd@picb.ac.cn) |
| 英文摘要 | Motivation: to understand transcription regulatory mechanisms, it is indispensable to investigate transcription factor (tf) dna binding preferences. we noted that the generally acknowledged information of functional annotations of tfs as well as that of their target genes should provide useful hints in determining tf dna binding preferences. results: in this contribution, we developed an integrative method based on the nearest neighbor algorithm, to predict dna binding preferences through integrating both the functional/ structural information of tfs and the interaction between tfs and their targets. the accuracy of cross-validation tests on the dataset consisting of 3430 positive samples and 7000 negative samples reaches 87.0% for 10-fold cross-validation and 87.9% for jackknife cross-validation test, which is a much better result than that in our previous work. the prediction result indicates that the improved method we developed could be a powerful approach to infer the tf dna preference in silico. |
| WOS关键词 | DOMAIN COMPOSITION ; DISCOVERY ; SEQUENCES ; DATABASE |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| WOS类目 | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
| 语种 | 英语 |
| WOS记录号 | WOS:000249818700013 |
| 出版者 | OXFORD UNIV PRESS |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2380361 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Cai, Yu-Dong |
| 作者单位 | 1.Chinese Acad Sci, Shanghai Inst Biol Sci, CAS MPG Partner Inst Computat Biol, Beijing 100039, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Biolog Sci, Bioinformat Ctr, Key Lab Mol Syst Biol, Shanghai 200031, Peoples R China 4.Univ Manchester, Inst Sci & Technol, Dept Math, Manchester M60 1QD, Lancs, England 5.Shanghai Ctr Bioinformat Technol, 200235 Shanghai, Peoples R China 6.Shanghai Jiao Tong Univ, Coll Life Sci & Biotechnol, Shanghai, Peoples R China 7.Queens Med Res Inst, Ctr Cardiovasc Sci, Phys Mol Lab, Edinburgh, Midlothian, Scotland |
| 推荐引用方式 GB/T 7714 | Qian, Ziliang,Lu, Lingyi,Liu, XiaoJun,et al. An approach to predict transcription factor dna binding site specificity based upon gene and transcription factor functional categorization[J]. Bioinformatics,2007,23(18):2449-2454. |
| APA | Qian, Ziliang,Lu, Lingyi,Liu, XiaoJun,Cai, Yu-Dong,&Li, Yixue.(2007).An approach to predict transcription factor dna binding site specificity based upon gene and transcription factor functional categorization.Bioinformatics,23(18),2449-2454. |
| MLA | Qian, Ziliang,et al."An approach to predict transcription factor dna binding site specificity based upon gene and transcription factor functional categorization".Bioinformatics 23.18(2007):2449-2454. |
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来源：中国科学院大学
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