作者
Justin K Huang, Daniel E Carlin, Michael Ku Yu, Wei Zhang, Jason F Kreisberg, Pablo Tamayo, Trey Ideker
发表日期
2018/4/25
期刊
Cell systems
卷号
6
期号
4
页码范围
484-495. e5
出版商
Elsevier
简介
Gene networks are rapidly growing in size and number, raising the question of which networks are most appropriate for particular applications. Here, we evaluate 21 human genome-wide interaction networks for their ability to recover 446 disease gene sets identified through literature curation, gene expression profiling, or genome-wide association studies. While all networks have some ability to recover disease genes, we observe a wide range of performance with STRING, ConsensusPathDB, and GIANT networks having the best performance overall. A general tendency is that performance scales with network size, suggesting that new interaction discovery currently outweighs the detrimental effects of false positives. Correcting for size, we find that the DIP network provides the highest efficiency (value per interaction). Based on these results, we create a parsimonious composite network with both high efficiency …
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