Cellular phenotype recognition for high-content RNA interference genome-wide screening

Jun Wang, Xiaobo Zhou, Pamela L. Bradley, Shih Fu Chang, Norbert Perrimon, Stephen T.C. Wong

Research output: Contribution to journalArticlepeer-review

53 Scopus citations

Abstract

Genome-wide, cell-based screens using high-content screening (HCS) techniques and automated fluorescence microscopy generate thousands of high-content images that contain an enormous wealth of cell biological information. Such screens are key to the analysis of basic cell biological principles, such as control of cell cycle and cell morphology. However, these screens will ultimately only shed light on human disease mechanisms and potential cures if the analysis can keep up with the generation of data. A fundamental step toward automated analysis of high-content screening is to construct a robust platform for automatic cellular phenotype identification. The authors present a framework, consisting of microscopic image segmentation and analysis components, for automatic recognition of cellular phenotypes in the context of the Rho family of small GTPases. To implicate genes involved in Rac signaling, RNA interference (RNAi) was used to perturb gene functions, and the corresponding cellular phenotypes were analyzed for changes. The data used in the experiments are high-content, 3-channel, fluorescence microscopy images of Drosophila Kc167 cultured cells stained with markers that allow visualization of DNA, polymerized actin filaments, and the constitutively activated Rho protein RacV12. The performance of this approach was tested using a cellular database that contained more than 1000 samples of 3 predefined cellular phenotypes, and the generalization error was estimated using a cross-validation technique. Moreover, the authors applied this approach to analyze the whole high-content fluorescence images of Drosophila cells for further HCS-based gene function analysis.

Original languageEnglish (US)
Pages (from-to)29-39
Number of pages11
JournalJournal of Biomolecular Screening
Volume13
Issue number1
DOIs
StatePublished - Feb 2008

Keywords

  • High-content screening
  • Microscopic image segmentation
  • Phenotype classification
  • Phenotype feature extraction and selection
  • RNA interference

ASJC Scopus subject areas

  • Analytical Chemistry
  • Clinical Biochemistry
  • Biotechnology
  • Biochemistry
  • Molecular Biology

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