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Quantifying modularity in the evolution of biomolecular systems.

Berend Snel1, Martijn A Huynen

  • 1Nijmegen Center for Molecular Life Sciences, p/a Centre for Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands. b.snel@cmbi.kun.nl

Genome Research
|March 3, 2004
PubMed
Summary
This summary is machine-generated.

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Functional modules in biomolecular systems often lack evolutionary cohesion across genomes. While some exhibit significant modularity, many show flexibility due to gene function differences, not definition noise.

Area of Science:

  • Genomics
  • Systems Biology
  • Evolutionary Biology

Background:

  • Functional modules are key components of biomolecular systems.
  • Their cohesive behavior across different genomes (evolutionary modularity) is not well understood.

Purpose of the Study:

  • To investigate the extent to which functional modules act as evolutionary modules.
  • To analyze the phyletic patterns of genes within functional modules across multiple genomes.

Main Methods:

  • Analysis of gene phyletic patterns for a large set of functional modules.
  • Comparative genomics across 110 genomes.
  • Assessment of functional differentiation within orthologous gene groups.

Main Results:

Related Experiment Videos

  • Most functional modules exhibit limited evolutionary modularity.
  • Interspecies flexibility is largely due to functional differentiation within gene orthologs.
  • Approximately half of the modules show significantly more modularity than random gene sets after filtering.
  • Biosynthetic pathways are more evolutionarily modular than catabolic pathways within the EcoCyc database.

    • Conclusions:

    • Functional modules are not always cohesive evolutionary units.
    • Functional differentiation within genes plays a significant role in the observed flexibility.
    • Differences in module definitions complicate cross-collection comparisons, but within-collection analyses reveal significant evolutionary modularity patterns.