A Systems Approach to Mapping DNA Damage Response Pathways

By F. Kawasaki, B. Zou, X. Xu, R. Ordway, J. Trommershauser, R. Schneggenburger, A. Zippelius. 2006

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Protein networks in disease. (2008, background): “In yeast, genetic perturbations have been profiled by expression profiling of gene knockout strains (Hughes et al. 2000; Workman et al. 2006; Hu et al. 2007) or by analysis of expression quantitative trait loci (eQTLs) (Brem and Kruglyak 2005), which identifies associations between polymorphic genom”
How to infer gene networks from expression profiles (2007, background): “These algorithms will become more ‘integrative’ by exploiting, in addition to expression profiles, protein–protein interaction data, sequence data, protein modification data, metabolic data and more, in the inference process”
Differential network biology (2012, unknown): “Workman et al (2006) performed a ChIP-CHIP study focused speciﬁcally on the changes in transcriptional wiring that occur with respect to yeast transcription factor binding after exposure to the DNA damaging agent methyl methane-sulfonate (MMS), for 30 different transcription factors.”