PPI database：STRING VS IntAct VS IMEx

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PPI database：STRING VS IntAct VS IMEx

1. 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
2. Henning et al, IntAct: an open source molecular interaction database, Nucleic Acids Research, Volume 32, Issue suppl_1, 1 January 2004, Pages D452–D455,
3. 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