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Protein Networks and Pathway Analysis

Volume 563 of the series Methods in Molecular Biology pp 275-287

Date:

High-Throughput siRNA Screening as a Method of Perturbation of Biological Systems and Identification of Targeted Pathways Coupled with Compound Screening

  • Jeff KieferAffiliated withPharmaceutical Genomics Division, Translational Genomics Research Institute (TGen) Email author 
  • , Hongwei H. YinAffiliated withPharmaceutical Genomics Division, Translational Genomics Research Institute (TGen)
  • , Qiang Q. QueAffiliated withPharmaceutical Genomics Division, Translational Genomics Research Institute (TGen)
  • , Spyro MoussesAffiliated withPharmaceutical Genomics Division, Translational Genomics Research Institute (TGen)

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Abstract

High-throughput RNA interference (HT-RNAi) is a powerful research tool for parallel, ‘genome-wide’, targeted knockdown of specific gene products. Such perturbation of gene product expression allows for the systematic query of gene function. The phenotypic results can be monitored by assaying for specific alterations in molecular and cellular endpoints, such as promoter activation, cell proliferation and survival. RNAi profiling may also be coupled with drug screening to identify molecular correlates of drug response. As with other genomic-scale data, methods of data analysis are required to handle the unique aspects of data normalization and statistical processing. In addition, novel techniques or knowledge-mining strategies are required to extract useful biological information from HT-RNAi data. Knowledge-mining strategies involve the novel application of bioinformatic tools and expert curation to provide biological context to genomic-scale data such as that generated from HT-RNAi data. Pathway-based tools, whether text-mining based or manually curated, serve an essential role in knowledge mining. These tools can be applied during all steps of HT-RNAi screen experiments including pre-screen knowledge gathering, assay development and hit confirmation and validation. Most importantly, pathway tools allow the interrogation of HT-RNAi data to identify and prioritize pathway-based biological information as a result of specific loss of gene function.

Key words

RNAi high-throughput RNAi screening text-mining pathway analysis