How to understand the cell by breaking it: network analysis of gene perturbation screens

Details How to understand the cell by breaking it: network analysis of gene perturbation screens How to understand the cell by breaking it: network analysis of gene perturbation screens

2009-10-15

arxiv.org/abs/0910.2938v2

PLoS Comp Bio, 2010 Feb 26;6(2):e1000655

Biology

Quantitative Biology

Molecular Networks

Review based on ISMB 2009 tutorial; after two rounds of revision

Scientific paper

10.1371/journal.pcbi.1000655

Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental perturbations on a genome-wide scale. This review surveys the current state-of-the-art in analyzing perturbation screens from a network point of view. We describe approaches to make the step from the parts list to the wiring diagram by using phenotypes for network inference and integrating them with complementary data sources. The first part of the review describes methods to analyze one- or low-dimensional phenotypes like viability or reporter activity; the second part concentrates on high-dimensional phenotypes showing global changes in cell morphology, transcriptome or proteome.

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