SANTA：量化分子网络的功能含量
SANTA: quantifying the functional content of molecular networks
摘要：
将分子相互作用网络与细胞功能和表型联系起来是系统生物学的一个关键目标。在这里，我们采用空间统计的概念来评估分子网络的功能内容。基于关联内疚原理，我们的方法（称为SANTA）量化了基因集和网络之间的关联强度，并像其他富集方法注释基因列表一样功能性地注释分子网络。作为一般关联度量，SANTA可以（i）使用策展的基因集的集合在功能上注释实验衍生的网络，以及（ii）使用策展的网络的集合注释实验衍生的基因集，以及（iii）对基因进行优先级排序以进行后续分析。我们使用\emph{S. cerevisiae}遗传相互作用网络和癌细胞系中的全基因组RNAi筛选在几个案例研究中验证了SANTA的功效。我们的理论，模拟和应用表明，SANTA提供了一个原则性的统计方法来量化分子网络和细胞功能和表型之间的关联。SANTA可从http://bioconductor.org/packages/release/bioc/html/SANTA.html获得。
英文摘要：
Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the guilt-by-association principle, our approach (called SANTA) quantifies the strength of association between a gene set and a network, and functionally annotates molecular networks like other enrichment methods annotate lists of genes. As a general association measure, SANTA can (i) functionally annotate experimentally derived networks using a collection of curated gene sets, and (ii) annotate experimentally derived gene sets using a collection of curated networks, as well as (iii) prioritize genes for follow-up analyses. We exemplify the efficacy of SANTA in several case studies using the \emph{S. cerevisiae} genetic interaction network and genome-wide RNAi screens in cancer cell lines. Our theory, simulations and applications show that SANTA provides a principled statistical way to quantify the association between molecular networks and cellular functions and phenotypes. SANTA is available from http://bioconductor.org/packages/release/bioc/html/SANTA.html.
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