Saturday, 20 December 2014

SANTA - Spatial Analysis of NeTwork Associations

A festive bioinformatics acronym today: SANTA - Spatial Analysis of NeTwork Associations. The authors don't make a big deal of the acronym in the paper but it seemed contrived enough for a Christmas ORCA entry.


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 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​/bioc/html/SANTA.html.

Ref: Cornish AJ & Markowetz F (2014) SANTA: Quantifying the Functional Content of Molecular Networks. PLoS Comput Biol 10(9): e1003808.

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