2013
DOI: 10.1016/j.semcancer.2013.06.004
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Integrated network analyses for functional genomic studies in cancer

Abstract: RNA-interference (RNAi) studies hold great promise for functional investigation of the significance of genetic variations and mutations, as well as potential synthetic lethalities, for understanding and treatment of cancer, yet technical and conceptual issues currently diminish the potential power of this approach. While numerous research groups are usefully employing this kind of functional genomic methodology to identify molecular mediators of disease severity, response, and resistance to treatment, findings… Show more

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Cited by 14 publications
(11 citation statements)
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“…Proposed mechanisms for repression include GR tethering to and inhibiting growth induction transcription factors through protein-protein interactions or by interactions with growth induction transcription factors at composite GREs [ Yamamoto et al, 1998 ]. However, despite extensive gene expression array analyses, specific genes that mediate cell death have not been well defined, perhaps in part because recent data support GCs acting through the GR to impact a complex network of activators [ Beato et al, 1995 ; Hollenberg et al, 1985 ] [ Martin, 2003 ; Wilson et al, 2013 ].…”
Section: Introductionmentioning
confidence: 99%
“…Proposed mechanisms for repression include GR tethering to and inhibiting growth induction transcription factors through protein-protein interactions or by interactions with growth induction transcription factors at composite GREs [ Yamamoto et al, 1998 ]. However, despite extensive gene expression array analyses, specific genes that mediate cell death have not been well defined, perhaps in part because recent data support GCs acting through the GR to impact a complex network of activators [ Beato et al, 1995 ; Hollenberg et al, 1985 ] [ Martin, 2003 ; Wilson et al, 2013 ].…”
Section: Introductionmentioning
confidence: 99%
“…Two recent changes occurred: model systems have started to include enormous data volumes (big data), leading network inference approaches to unprecedented sophistication (multilayer networks). Generalizations such as reciprocal engineering (the interactome scaffold connecting pieces of experimental evidence and determining the target pathways), and forward engineering (pathway modulation used to analyze downstream phenotypes) ( 55 ). More importantly, controllability has emerged as a paradigmatic example of research direction with almost ubiquitous applications.…”
Section: Discussionmentioning
confidence: 99%
“…To cite a few examples, RNAi screens are useful for uncovering synthetic lethal relationships, 54 genes associated with homologous recombination, 55 and genes responsible for ectodomain shedding. 56 Many have promoted the value of data integration analysis methods, 2,4,8,21 however, these analysis approaches remain under utilized in the gene interference community.…”
Section: Discussionmentioning
confidence: 99%