[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.

Publisher Info

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

Download reference. The following formats are available: HTML (with abstract), plain text (with abstract), BibTeX, RIS (EndNote, RefMan, ProCite), ReDIF
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

For technical questions regarding this item, or to correct its listing, contact: (Thomas Krichel).

Related research

Keywords: Genomics; reverse engineering; microarray;

Other versions of this item:

Statistics

Access and download statistics

Did you know? You can import bibliographic info in various formats into you bibliographic tool, or just into your word processor. See under "publisher info" on each abstract page.

This page was last updated on 2009-10-24.