A novel computational method to predict transcription factor dna binding preference
文献类型：期刊论文
| 作者 | Qian, Ziliang; Cai, Yu-Dong; Li, Yixue |
| 刊名 | Biochemical and biophysical research communications
 |
| 出版日期 | 2006-09-29 |
| 卷号 | 348期号:3页码:1034-1037 |
| 关键词 | Transcription factor Transcription factor dna binding preference Nearest neighbor algorithm 0/1 system Jackknife cross-validation test Gene ontology |
| ISSN号 | 0006-291X |
| DOI | 10.1016/j.bbrc.2006.07.149 |
| 通讯作者 | Cai, yu-dong(cyd@picb.ac.cn) |
| 英文摘要 | Transcription factor binds to sequence specific sites in regulatory region to control nearby gene's expression. it is termed as the major regulator of transcription. however, identifying dna binding preference of transcription factors systematically is still a challenge. by using the nearest neighbor algorithm, a novel computational approach was developed to predict transcription factor dna binding preference based on the gene ontology [m. ashburner, c.a. ball, j.a. blake, d. botstein, h. butler, j.m. cherry, a.p. davis, k. dolinski, s.s. dwight, j.t. eppig, m.a. harris, d.p. hill, l. issel-tarver, a. kasarskis, s. lewis, j.c. matese, j.e. richardson, m. ringwald, g.m. rubin, g. sherlock, gene ontology: tool for the unification of biology, nat. genet. 25 (2000) 25-29.] and 0/1 encoding system of nucleotide. the overall success rate of jackknife cross-validation test for our predictor reaches 76.6%, which indicates the dna binding preference is closely correlated with its biological functions and computational method developed in this contribution could be a powerful tool to investigate transcription factor dna binding preference, especially for those novel transcription factors with little prior knowledge on its dna binding preference. (c) 2006 elsevier inc. all rights reserved. |
| WOS关键词 | FUNCTIONAL DOMAIN COMPOSITION ; HYBRIDIZATION SPACE ; GENE ONTOLOGY ; PROTEINS ; SITES ; RECOGNITION ; DISCOVERY ; FAMILY ; CODE ; GO |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics |
| WOS类目 | Biochemistry & Molecular Biology ; Biophysics |
| 语种 | 英语 |
| WOS记录号 | WOS:000240166500035 |
| 出版者 | ACADEMIC PRESS INC ELSEVIER SCIENCE |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2379515 |
| 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, MPG Partner Int Computat Biol, Beijing 100864, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Bioinformat Ctr, Shanghai 200031, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 4.Univ Manchester, Inst Sci & Technol, Dept Math, Manchester M60 1QD, Lancs, England 5.Shanghai Ctr Bioinformat Technol, Shanghai 200235, Peoples R China |
| 推荐引用方式 GB/T 7714 | Qian, Ziliang,Cai, Yu-Dong,Li, Yixue. A novel computational method to predict transcription factor dna binding preference[J]. Biochemical and biophysical research communications,2006,348(3):1034-1037. |
| APA | Qian, Ziliang,Cai, Yu-Dong,&Li, Yixue.(2006).A novel computational method to predict transcription factor dna binding preference.Biochemical and biophysical research communications,348(3),1034-1037. |
| MLA | Qian, Ziliang,et al."A novel computational method to predict transcription factor dna binding preference".Biochemical and biophysical research communications 348.3(2006):1034-1037. |
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来源：中国科学院大学
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