Skip to main content
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Rights and Permissions
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian
  • Log in
  • My Cart

Main menu

  • Home
  • Articles
    • Current
    • Latest Articles
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • Archive
  • Front Matter
  • News
    • For the Press
    • Highlights from Latest Articles
    • PNAS in the News
  • Podcasts
  • Authors
    • Purpose and Scope
    • Editorial and Journal Policies
    • Submission Procedures
    • For Reviewers
    • Author FAQ
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Rights and Permissions
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian

User menu

  • Log in
  • My Cart

Search

  • Advanced search
Home
Home

Advanced Search

  • Home
  • Articles
    • Current
    • Latest Articles
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • Archive
  • Front Matter
  • News
    • For the Press
    • Highlights from Latest Articles
    • PNAS in the News
  • Podcasts
  • Authors
    • Purpose and Scope
    • Editorial and Journal Policies
    • Submission Procedures
    • For Reviewers
    • Author FAQ

New Research In

Physical Sciences

Featured Portals

  • Physics
  • Chemistry
  • Sustainability Science

Articles by Topic

  • Applied Mathematics
  • Applied Physical Sciences
  • Astronomy
  • Computer Sciences
  • Earth, Atmospheric, and Planetary Sciences
  • Engineering
  • Environmental Sciences
  • Mathematics
  • Statistics

Social Sciences

Featured Portals

  • Anthropology
  • Sustainability Science

Articles by Topic

  • Economic Sciences
  • Environmental Sciences
  • Political Sciences
  • Psychological and Cognitive Sciences
  • Social Sciences

Biological Sciences

Featured Portals

  • Sustainability Science

Articles by Topic

  • Agricultural Sciences
  • Anthropology
  • Applied Biological Sciences
  • Biochemistry
  • Biophysics and Computational Biology
  • Cell Biology
  • Developmental Biology
  • Ecology
  • Environmental Sciences
  • Evolution
  • Genetics
  • Immunology and Inflammation
  • Medical Sciences
  • Microbiology
  • Neuroscience
  • Pharmacology
  • Physiology
  • Plant Biology
  • Population Biology
  • Psychological and Cognitive Sciences
  • Sustainability Science
  • Systems Biology

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger P. Alexander and Mark Gerstein
PNAS May 3, 2010. published ahead of print May 3, 2010. https://doi.org/10.1073/pnas.0914771107
Koon-Kiu Yan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gang Fang
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nitin Bhardwaj
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roger P. Alexander
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mark Gerstein
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  1. Edited* by Gregory A. Petsko, Brandeis University, Waltham, MA, and approved April 2, 2010 (received for review December 20, 2009)

  • Article
  • Figures & SI
  • Authors & Info
  • PDF
Loading

Abstract

The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell. To apply our firsthand knowledge of the architecture of software systems to understand cellular design principles, we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology and evolution. We show that both networks have a fundamentally hierarchical layout, but there is a key difference: The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. We further develop a way to measure evolutionary rates comparably between the two networks and explain this difference in terms of network evolution. The process of biological evolution via random mutation and subsequent selection tightly constrains the evolution of regulatory network hubs. The call graph, however, exhibits rapid evolution of its highly connected generic components, made possible by designers’ continual fine-tuning. These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems.

  • systems biology
  • adaptive complex systems

Footnotes

  • 1To whom correspondence should be addressed. E-mail: Mark.Gerstein{at}yale.edu.
  • Author contributions: K.-K.Y., G.F., N.B., R.P.A., and M.G. designed research; K.-K.Y. performed research; G.F., N.B., and R.P.A. contributed new reagents/analytic tools; K.-K.Y. analyzed data; and K.-K.Y. and M.G. wrote the paper.

  • The authors declare no conflict of interest.

  • *This Direct Submission article had a prearranged editor.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.0914771107/-/DCSupplemental.

Freely available online through the PNAS open access option.

Next
Back to top
Article Alerts
Email Article

Thank you for your interest in spreading the word on PNAS.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
(Your Name) has sent you a message from PNAS
(Your Name) thought you would like to see the PNAS web site.
Citation Tools
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger P. Alexander, Mark Gerstein
Proceedings of the National Academy of Sciences May 2010, DOI: 10.1073/pnas.0914771107

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger P. Alexander, Mark Gerstein
Proceedings of the National Academy of Sciences May 2010, DOI: 10.1073/pnas.0914771107
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Mendeley logo Mendeley

More Articles of This Classification

Biological Sciences

  • SAMHD1 enhances immunoglobulin hypermutation by promoting transversion mutation
  • Origin, antigenicity, and function of a secreted form of ORF2 in hepatitis E virus infection
  • A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy
Show more

Biophysics and Computational Biology

  • A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy
  • Cell contraction induces long-ranged stress stiffening in the extracellular matrix
  • Structural dynamics is a determinant of the functional significance of missense variants
Show more

Related Content

  • No related articles found.
  • Scopus
  • PubMed
  • Google Scholar

Cited by...

  • Evidence for soft bounds in Ubuntu package sizes and mammalian body masses
  • Universal distribution of component frequencies in biological and technological systems
  • Evolution of a modular software network
  • Unexpected Coregulator Range for the Global Regulator Lrp of Escherichia coli and Proteus mirabilis
  • Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators
  • Scopus (43)
  • Google Scholar

Similar Articles

You May Also be Interested in

Recent flooding events highlight why flood-risk governance in the United States needs a major overhaul. They also suggest why the necessary refocus on shared responsibility will not be easy.
Opinion: How to achieve better flood-risk governance in the United States
Recent flooding events highlight why flood-risk governance in the United States needs a major overhaul. They also suggest why the necessary refocus on shared responsibility will not be easy.
Image courtesy of Shutterstock/michelmond.
Bridget Scanlon discusses the use of global hydrologic models for studying changes in water storage worldwide.
Global hydrologic models and water storage
Bridget Scanlon discusses the use of global hydrologic models for studying changes in water storage worldwide.
Listen
Past PodcastsSubscribe
PNAS Profile of Dorothy L. Cheney and Robert M. Seyfarth.
PNAS Profile
PNAS Profile of Dorothy L. Cheney and Robert M. Seyfarth.
Researchers estimate the risk of infectious disease transmission on board transcontinental airline flights.
Infectious disease transmission on airplanes
Researchers estimate the risk of infectious disease transmission on board transcontinental airline flights.
Image courtesy of Pixabay/PublicDomainPictures.
Researchers report early evidence of Maya animal management.
Early Maya animal rearing and trade
Researchers report early evidence of Maya animal management.
Proceedings of the National Academy of Sciences: 115 (16)
Current Issue

Submit

Sign up for Article Alerts

Jump to section

  • Article
  • Figures & SI
  • Authors & Info
  • PDF
Site Logo
Powered by HighWire
  • Submit Manuscript
  • Twitter
  • Facebook
  • RSS Feeds
  • Email Alerts

Articles

  • Current Issue
  • Latest Articles
  • Archive

PNAS Portals

  • Classics
  • Front Matter
  • Teaching Resources
  • Anthropology
  • Chemistry
  • Physics
  • Sustainability Science

Information for

  • Authors
  • Reviewers
  • Press

Feedback    Privacy/Legal

Copyright © 2018 National Academy of Sciences.