Inpreppi: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes | |
Sun, Jingchun1,2; Sun, Yan3,4; Ding, Guohui3,4; Liu, Qi5; Wang, Chuan3; He, Youyu3; Shi, Tieliu3; Li, Yixue3; Zhao, Zhongming1,2,6,7 | |
刊名 | Bmc bioinformatics |
2007-10-26 | |
卷号 | 8页码:10 |
ISSN号 | 1471-2105 |
DOI | 10.1186/1471-2105-8-414 |
通讯作者 | Zhao, zhongming(zzhao@vcu.edu) |
英文摘要 | Background: although many genomic features have been used in the prediction of protein-protein interactions (ppis), frequently only one is used in a computational method. after realizing the limited power in the prediction using only one genomic feature, investigators are now moving toward integration. so far, there have been few integration studies for ppi prediction; one failed to yield appreciable improvement of prediction and the others did not conduct performance comparison. it remains unclear whether an integration of multiple genomic features can improve the ppi prediction and, if it can, how to integrate these features. results: in this study, we first performed a systematic evaluation on the ppi prediction in escherichia coli (e. coli) by four genomic context based methods: the phylogenetic profile method, the gene cluster method, the gene fusion method, and the gene neighbor method. the number of predicted ppis and the average degree in the predicted ppi networks varied greatly among the four methods. further, no method outperformed the others when we tested using three well-defined positive datasets from the kegg, ecocyc, and dip databases. based on these comparisons, we developed a novel integrated method, named inpreppi. inpreppi first normalizes the ac value (an integrated value of the accuracy and coverage) of each method using three positive datasets, then calculates a weight for each method, and finally uses the weight to calculate an integrated score for each protein pair predicted by the four genomic context based methods. we demonstrate that inpreppi outperforms each of the four individual methods and, in general, the other two existing integrated methods: the joint observation method and the integrated prediction method in string. these four methods and inpreppi are implemented in a user-friendly web interface. conclusion: this study evaluated the ppi prediction by four genomic context based methods, and presents an integrated evaluation method that shows better performance in e. coli. |
WOS关键词 | PHYLOGENETIC PROFILES ; FUNCTIONAL LINKAGES ; INTERACTION MAP ; NEIGHBORING GENES ; NETWORK ; ORGANISMS ; COEXPRESSION ; ORGANIZATION ; PROTEOMICS ; DATABASE |
WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology |
WOS类目 | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology |
语种 | 英语 |
出版者 | BIOMED CENTRAL LTD |
WOS记录号 | WOS:000252960300001 |
内容类型 | 期刊论文 |
URI标识 | http://www.corc.org.cn/handle/1471x/2380456 |
专题 | 中国科学院大学 |
通讯作者 | Zhao, Zhongming |
作者单位 | 1.Virginia Commonwealth Univ, Virginia Inst Psychiat & Behav Genet, Richmond, VA 23298 USA 2.Virginia Commonwealth Univ, Dept Psychiat, Richmond, VA 23298 USA 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Bioinformat Ctr, Shanghai 200031, Peoples R China 4.Chinese Acad Sci, Grad Sch, Shanghai 200031, Peoples R China 5.Shanghai Jiao Tong Univ, Sch Life Sci & Technol, Shanghai 200240, Peoples R China 6.Virginia Commonwealth Univ, Dept Human Genet, Richmond, VA 23298 USA 7.Virginia Commonwealth Univ, Ctr Study Biol Complex, Richmond, VA 23284 USA |
推荐引用方式 GB/T 7714 | Sun, Jingchun,Sun, Yan,Ding, Guohui,et al. Inpreppi: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes[J]. Bmc bioinformatics,2007,8:10. |
APA | Sun, Jingchun.,Sun, Yan.,Ding, Guohui.,Liu, Qi.,Wang, Chuan.,...&Zhao, Zhongming.(2007).Inpreppi: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.Bmc bioinformatics,8,10. |
MLA | Sun, Jingchun,et al."Inpreppi: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes".Bmc bioinformatics 8(2007):10. |
个性服务 |
查看访问统计 |
相关权益政策 |
暂无数据 |
收藏/分享 |
除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。
修改评论