Advanced Search
MyIDEAS: Login to save this paper or follow this series

How to Reconstruct a Large Genetic Network from

Contents:

Author Info

  • How to Reconstruct a Large Genetic Network from n Gene Perturbations in Fewer than n2 Easy Steps
Registered author(s):

    Abstract

    n Gene Perturbations in Fewer than n2 Easy Steps [gzipped postscript] [postscript] [pdf] Andreas Wagner I present an algorithm to reconstruct direct regulatory interactions in gene networks from the effects of genetic perturbations on gene activity. Genomic technology has made feasible large-scale experiments that perturb the activity of many genes and then assess the effect of each individual perturbation on all other genes in an organism. Current experimental techniques can not distinguish between direct and indirect effects of a genetic perturbation. An example of an indirect effect is a gene X encoding a protein kinase, which phosphorylates and activates a transcription factor Y, which then activates transcription of gene Z. X influences the activity of gene Y directly, whereas it influences Z indirectly. To reconstruct a genetic network means to identify, for each gene and within the limits of experimental resolution, the direct effects of a perturbed gene on other genes. One can think of this as identifying the causal structure of the network. I introduce an algorithm that performs this task for networks of arbitrary size and complexity. It is based on a graph representation of a genetic network. Algorithmic complexity in both storage and time is low, less than O(n2). In practice, the algorithm can reconstruct networks of several thousand genes in mere CPU seconds on a desktop workstation.

    Download Info

    To our knowledge, this item is not available for download. To find whether it is available, there are three options:
    1. Check below under "Related research" whether another version of this item is available online.
    2. Check on the provider's web page whether it is in fact available.
    3. Perform a search for a similarly titled item that would be available.

    Bibliographic Info

    Paper provided by Santa Fe Institute in its series Working Papers with number 01-09-047.

    as in new window
    Length:
    Date of creation: Sep 2001
    Date of revision:
    Handle: RePEc:wop:safiwp:01-09-047

    Contact details of provider:
    Postal: 1399 Hyde Park Road, Santa Fe, New Mexico 87501
    Web page: http://www.santafe.edu/sfi/publications/working-papers.html
    More information through EDIRC

    Related research

    Keywords: Genomics; reverse engineering; microarray;

    This paper has been announced in the following NEP Reports:

    References

    References listed on IDEAS
    Please report citation or reference errors to , or , if you are the registered author of the cited work, log in to your RePEc Author Service profile, click on "citations" and make appropriate adjustments.:
    as in new window
    1. Andreas Wagner & David Fell, 2000. "The Small World Inside Large Metabolic Networks," Working Papers 00-07-041, Santa Fe Institute.
    2. Andreas Wagner, 2001. "The Yeast Protein Interaction Network Evolves Rapidly and Contains Few Redundant Duplicate Genes," Working Papers 01-04-022, Santa Fe Institute.
    Full references (including those not matched with items on IDEAS)

    Citations

    Lists

    This item is not listed on Wikipedia, on a reading list or among the top items on IDEAS.

    Statistics

    Access and download statistics

    Corrections

    When requesting a correction, please mention this item's handle: RePEc:wop:safiwp:01-09-047. See general information about how to correct material in RePEc.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: (Thomas Krichel).

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If references are entirely missing, you can add them using this form.

    If the full references list an item that is present in RePEc, but the system did not link to it, you can help with this form.

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your profile, as there may be some citations waiting for confirmation.

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.