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1.  Gene-centered regulatory networks 
Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a ‘systems level’ (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions between genes and their regulators. In the past years, significant progress has been made toward the mapping of GRNs using a variety of experimental and computational approaches. Here, we will discuss gene-centered approaches that we employed to characterize GRNs and describe insights that we have obtained into the global design principles of gene regulation in complex metazoan systems.
doi:10.1093/bfgp/elp049
PMCID: PMC3096532  PMID: 20008400
transcription factor; differential gene expression; gene-centered; gene regulatory network; yeast one-hybrid assay; Caenorhabditis elegans
2.  Quantitative cell array screening to identify regulators of gene expression 
In the last decade or so, advances in genome-scale technologies have allowed systematic and detailed analysis of gene function. The experimental accessibility of budding yeast makes it a test-bed for technology development and application of new functional genomic tools and resources that pave the way for comparable efforts in higher eukaryotes. In this article, we review advances in reporter screening technology to discover trans-acting regulators of promoters (or cis-elements) of interest in the context of a novel functional genomics approach called Reporter Synthetic Genetic Array (R-SGA) analysis. We anticipate that this methodology will enable researchers to collect quantitative data on hundreds of gene expression pathways in an effort to better understand transcriptional regulatory networks.
doi:10.1093/bfgp/elp047
PMCID: PMC3097099  PMID: 19952074
gene expression; reporter gene; Saccharomyces cerevisiae; cell cycle; histone gene
3.  Insights to transcriptional networks by using high throughput RNAi strategies 
RNA interference (RNAi) is a powerful method to unravel the role of a given gene in eukaryotic cells. The development of high throughput assay platforms such as fluorescence plate readers and high throughput microscopy has allowed the design of genome wide RNAi screens to systemically discern members of regulatory networks around various cellular processes. Here we summarize the different strategies employed in RNAi screens to reveal regulators of transcriptional networks. We focus our discussion in experimental approaches designed to uncover regulatory interactions modulating transcription factor activity.
doi:10.1093/bfgp/elp046
PMCID: PMC3097102  PMID: 19952073
RNAi screen; transcription factor; reporter; localization; post-translational modification

Results 1-3 (3)