A knowledge-based method to predict the cooperative relationship between transcription factors
文献类型：期刊论文
| 作者 | Lu, Lingyi2,3; Qian, Ziliang2,3; Shi, XiaoHe4; Li, Haipeng1; Cai, Yu-Dong5,6; Li, Yixue2,7 |
| 刊名 | Molecular diversity
 |
| 出版日期 | 2010-11-01 |
| 卷号 | 14期号:4页码:815-819 |
| 关键词 | Transcription factor cooperation Functional domain composition The nearest neighbor algorithm Jackknife cross-validation test Blast Amino acid composition |
| ISSN号 | 1381-1991 |
| DOI | 10.1007/s11030-009-9177-1 |
| 通讯作者 | Li, haipeng(lihaipeng@picb.ac.cn) |
| 英文摘要 | Identifying the cooperation between transcription factors is crucial and challenging to uncover the mystery behind the complex gene expression patterns. computational methods aimed to infer transcription factor cooperation are expected to get good results if we can integrate the knowledge (existed functional/structural annotations) of proteins. in this contribution, we proposed an information integrative computational framework to infer the cooperation between transcription factors, which relies on the hybridization-space method that can integrate the annotation information of proteins. in our computational experiments, by using function domain annotations only, on our testing dataset, the overall prediction accuracy and the specificity reaches 84.3% and 76.9%, respectively, which is a fairly good result and outperforms the prediction by both amino acid composition-based method and blast-based approach. the corresponding online service tfips (transcription factor interaction prediction system) is available on http://pcal.biosino.org/cgi-bin/tfips/tfips.pl. |
| WOS关键词 | FUNCTIONAL DOMAIN COMPOSITION ; PROTEIN-PROTEIN INTERACTIONS ; AMINO ACID COMPOSITION ; C-JUN ; SACCHAROMYCES-CEREVISIAE ; HYBRIDIZATION SPACE ; GENE ; ATF2 ; INTERPROSCAN ; ROLES |
| WOS研究方向 | Biochemistry & Molecular Biology ; Chemistry ; Pharmacology & Pharmacy |
| WOS类目 | Biochemistry & Molecular Biology ; Chemistry, Applied ; Chemistry, Medicinal ; Chemistry, Multidisciplinary |
| 语种 | 英语 |
| WOS记录号 | WOS:000284598600021 |
| 出版者 | SPRINGER |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2406650 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Li, Haipeng |
| 作者单位 | 1.Chinese Acad Sci, Shanghai Inst Biol Sci, CAS MPG Partner Inst Computat Biol, Shanghai 200031, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Mol Syst Biol, Shanghai 200031, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 4.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200025, Peoples R China 5.Shanghai Univ, Inst Syst Biol, Shanghai 200244, Peoples R China 6.Fudan Univ, Ctr Computat Syst Biol, Shanghai 200433, Peoples R China 7.Shanghai Ctr Bioinformat Technol, Shanghai 200235, Peoples R China |
| 推荐引用方式 GB/T 7714 | Lu, Lingyi,Qian, Ziliang,Shi, XiaoHe,et al. A knowledge-based method to predict the cooperative relationship between transcription factors[J]. Molecular diversity,2010,14(4):815-819. |
| APA | Lu, Lingyi,Qian, Ziliang,Shi, XiaoHe,Li, Haipeng,Cai, Yu-Dong,&Li, Yixue.(2010).A knowledge-based method to predict the cooperative relationship between transcription factors.Molecular diversity,14(4),815-819. |
| MLA | Lu, Lingyi,et al."A knowledge-based method to predict the cooperative relationship between transcription factors".Molecular diversity 14.4(2010):815-819. |
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来源：中国科学院大学
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