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A novel analysis of gene array data: yeast cell cycle.

Lawrence Sirovich1

  • 1Center for Physics and Biology, Rockefeller University, New York, NY, USA.

Biology Methods & Protocols
|December 30, 2020
PubMed
Summary
This summary is machine-generated.

This study identifies cell division cycle (CDC) genes in yeast using dynamic mode decomposition (DMD) directly from gene array data. The novel approach reveals hundreds of new CDC genes, advancing yeast cell cycle research.

Keywords:
S. Cerevisiae modelcell division cycledynamic mode decomposition

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Area of Science:

  • Systems Biology
  • Genomics
  • Molecular Biology

Background:

  • Previous yeast cell cycle studies relied on laboratory experiments.
  • Gene array data offers a rich source for understanding cellular dynamics.
  • Identifying cell division cycle (CDC) genes is crucial for understanding cell proliferation.

Purpose of the Study:

  • To determine cell division cycle (CDC) genes solely from gene array data using a novel computational method.
  • To analyze the dynamics of approximately 6000 yeast genes within a reduced-dimensional space.
  • To identify both known and previously undiscovered CDC genes.

Main Methods:

  • Adaptation of dynamic mode decomposition (DMD), a method originally used for turbulent flow analysis.
  • Analysis of gene array data to infer underlying gene dynamics.
  • Singular value decomposition to entangle gene dynamics, followed by DMD for disentanglement.

Main Results:

  • The dynamics of yeast genes can be described by a six-dimensional space, enabling precise determination of the cell cycle period.
  • Identification of known CDC genes with good agreement to existing literature.
  • Discovery of several hundred novel CDC genes that warrant further investigation.

Conclusions:

  • Dynamic mode decomposition (DMD) provides a powerful new tool for analyzing gene array signals.
  • This data-driven approach offers a new avenue for investigating the yeast cell cycle.
  • The newly identified CDC genes represent a significant expansion of our understanding of cell cycle regulation in yeast.