How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

Functional genomics has demonstratedconsiderable success in inferring the innerworking of a cell through analysis of itsresponse to various perturbations. Inrecent years several technological advanc-es have pushed gene perturbation screensto the forefront of functional genomics.Most importantly, modern technologiesmake it possible to probe gene function ona genome-wide scale in many modelorganisms and human. For example, largecollections of knock-out mutants play aprominent role in the study of Saccharomycescerevisiae [1], and RNA interference (RNAi)has become a widely used high-through-put method to knock-down target genes ina wide range of organisms, includingDrosophila melanogaster, Caenorhabditis elegans,and human [2–4].Another major advance is the develop-ment of rich phenotypic descriptions byimaging or measuring molecular featuresglobally. Observed phenotypes can revealwhich genes are essential for an organism,or work in a particular pathway, or have aspecific cellular function. Combining high-throughput screening techniques with richphenotypes enables researchers to observedetailed reactions to experimental pertur-bations on a genome-wide scale. Thismakes gene perturbation screens one ofthe most promising tools in functionalgenomics.Advances in the design and analysis ofgene perturbation screens may have animmediate impact on many areas ofbiological and medical research. Newscreening and phenotyping techniquesoften directly translate into new insightsin gene and protein functions. Results ofperturbation screens can also reveal unex-ploited areas of potential therapeuticintervention. For example, a recent RNAiscreen showed that some of the mostcritical protein kinases for the proliferationand survival of cancer cell lines are alsothe least studied [5].A goal becoming more and moreprominent in both experimental as wellas computational research is to leveragegene perturbation screens to the identifi-cation of molecular interactions, cellularpathways, and regulatory mechanisms.Research focus is shifting from under-standing the phenotypes of single proteinsto understanding how proteins fulfill theirfunction, what other proteins they interactwith, and where they act in a pathway.Novel ideas on how to use perturbationscreens to uncover cellular wiring dia-grams can lead to a better understandingof how cellular networks are deregulatedin diseases like cancer. This knowledge isindispensable for finding new drug targetsto attack the drivers of a disease and notonly the symptoms.This review surveys the current state-of-the-art in analyzing single gene perturba-tion screens from a network point of view.We describe approaches to make the stepfrom the parts list to the wiring diagram byusing phenotypes for network inferenceand integrating them with complementarydata sources.