SANTA

SANTA (Spatial Analysis of Network Associations) is a software tool that bridges molecular interaction networks with cellular functions and phenotypes, a fundamental objective in systems biology. By leveraging spatial statistics principles and guilt-by-association, SANTA offers a novel approach to quantifying the association strength between gene sets and networks, enabling the functional annotation of molecular networks like traditional enrichment methods annotate gene lists.

The versatility of SANTA is evident in its ability to (i) annotate experimental networks using curated gene sets, (ii) annotate experimentally derived gene sets using curated networks, and (iii) prioritize genes for further analysis. Through several case studies, including the S. cerevisiae genetic interaction network analysis and genome-wide RNAi screens in cancer cell lines, SANTA has demonstrated its effectiveness in providing meaningful statistical measures of association between networks and biological functions or phenotypes.