database:STRING VS IntAct VS IMEx"/>
PPI database:STRING VS IntAct VS IMEx
- S. Orchard et al., “Protein interaction data curation: The International Molecular Exchange (IMEx) consortium,” Nature Methods, vol. 9, no. 4, pp. 345-350, Apr 2012
- Henning et al, IntAct: an open source molecular interaction database, Nucleic Acids Research, Volume 32, Issue suppl_1, 1 January 2004, Pages D452–D455,
- Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein–protein interaction networks, integrated over the tree of life[J]. Nucleic acids research, 2015, 43(D1): D447-D452.
1. STRING
consolidating known and predicted protein–protein association data for a large number of organisms
STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically
meaningful.
data source:
- available experimental data on protein–protein interactions
- (i) systematic co-expression analysis,
- (ii) detection of shared selective signals across genomes,
- (iii) automated text-mining of the scientific literature
- (iv) computational transfer of interaction knowledge between organisms based on gene orthology.
小结:既有预测,又有实验数据,每一对蛋白给一个交互概率
关于查询:
是gene name 到gene name 的映射,输入蛋白Uniport accession number之后,需要手动确认映射是否正确
ID映射损失部分数据,选择物种的时候又会损失部分数据
查询到的蛋白交互对数据,不如IntAct中的多,且包含预测数据
2. IntAct
For a given protein, the binary view displays all its known interaction partners and their minimal textual description.
data source:
- mainly imported from large-scale experiments ,
- extracted from the literature by the IntAct and Swiss-Prot curation teams.
- submission of protein interaction data to IntAct in PSI MI format
小结:
蛋白对来源可靠
提供IMEx数据集下载
/
缺点:每次只能查找一个蛋白,返回这个蛋白相关的交互对
改进:编程实现批量查找蛋白交互对
3. IMEx
International Molecular Exchange (IMEx) consortium
European Molecular Biology Laboratory (EBI)
A non-redundant set of physical molecular interaction data from a broad taxonomic range of organisms.
最广泛,最全,最可靠,数据需要在IntAct 网站下载
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PPI database:STRING VS IntAct VS IMEx
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