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Fundamental patterns underlying gene expression profiles: simplicity from complexity.

N S Holter1, M Mitra, A Maritan

  • 1Department of Physics and Center for Materials Physics, 104 Davey Laboratory, Consortium, 519 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

Proceedings of the National Academy of Sciences of the United States of America
|July 13, 2000
PubMed
Summary
This summary is machine-generated.

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Gene expression changes across genomes are orchestrated by a few fundamental, robust patterns. These characteristic modes simplify complex transcriptional responses in organisms like yeast and humans.

Area of Science:

  • Genomics
  • Systems Biology
  • Bioinformatics

Background:

  • Gene expression data analysis often reveals complex temporal profiles.
  • Understanding the underlying principles of transcriptional regulation is crucial.

Purpose of the Study:

  • To identify fundamental patterns in DNA microarray gene expression data.
  • To determine if these patterns are conserved across different organisms.

Main Methods:

  • Analysis of published DNA microarray gene expression datasets.
  • Application of singular value decomposition (SVD) to identify temporal patterns.

Main Results:

  • Singular value decomposition uncovered underlying "characteristic modes" in gene expression temporal profiles.

Related Experiment Videos

  • A small number of these modes capture the essential features of expression profiles.
  • These fundamental patterns are conserved between yeast and human cells.

    • Conclusions:

    • Genome-wide transcriptional responses are orchestrated by a few simple, robust patterns.
    • These characteristic modes offer insights into the operation of genetic networks.
    • The findings reveal regularities in transcriptional transitions across diverse cell types.