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Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)
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Computational synchronization of microarray data with application to Plasmodium falciparum.

Wei Zhao1, Justin Dauwels, Jacquin C Niles

  • 1Singapore-MIT Alliance for Research and Technology, Centre for Life Sciences, 28 Medical Drive, Singapore 117456. jdauwels@ntu.edu.sg.

Proteome Science
|July 5, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to improve Plasmodium falciparum gene expression analysis from microarrays. The approach reconstructs clearer expression patterns, identifying key protein kinases regulating the intra-erythrocytic cycle.

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Area of Science:

  • Genomics
  • Parasitology
  • Bioinformatics

Background:

  • Microarrays are used to study Plasmodium falciparum blood stage infection.
  • Gene expression is measured over the 48-hour intra-erythrocytic cycle (IDC).
  • Cell population asynchrony blurs microarray measurements.

Purpose of the Study:

  • To develop a generalized deconvolution approach to reconstruct intrinsic gene expression patterns.
  • To apply this method to P. falciparum IDC microarray data.
  • To identify protein kinases involved in regulating P. falciparum IDC transitions.

Main Methods:

  • Developed a statistical model for synchrony decay.
  • Reconstructed expression patterns using statistical inference.
  • Handled noisy and missing microarray data.

Main Results:

  • Reconstructed profiles revealed clearer gene expression patterns.
  • Identified and ranked protein kinases by likelihood of involvement in IDC stage transitions.
  • Several protein kinases showed high probability rankings for regulating developmental transitions.

Conclusions:

  • Proposed a novel methodology for extracting intrinsic expression patterns from microarray data.
  • Predicted several protein kinases play significant roles in the P. falciparum IDC.
  • Suggests further functional analysis of these kinases may yield new insights into IDC regulation.