Automated Modeling of Signal Transduction Networks

Martin Steffen1, Allegra Petti1, Patrik D'haeseleer1,2, John Aach1,2, George Church1,2

1Dept. of Genetics and 2Lipper Center for Computational Genetics,
Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, 02115, USA.

BMC Bioinformatics 2002, 3:34

Supplemental Material

Last modified: November 1,2002


  1. Abstract
  2. Obtaining the NetSearch programs
  3. Run NetSearch
  4. Copyright
  5. Further assistance


Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. We have developed a computational approach for identifying signaling networks that employs protein-interaction maps generated from large-scale two-hybrid screens and expression profiles from DNA microarrays. Networks are determined entirely by integrating the protein-protein interaction data with the microarray expression data, without prior knowledge of pathway intermediates. We show that our technique accurately reconstructs MAP Kinase signaling networks in Saccharomyces cerevisiae. This general approach should enhance our ability to predict signaling networks and to discover new components of known networks.

Obtaining the NetSearch programs

Source code and executables for Win32 operating systems, and also source code that can be compiled under UNIX, are available here.

The Win32 executable can be run from a DOS or Command window. To compile the source code for UNIX, use the following command:
gcc -lm -o NetSearch NetSearch.c NetSdstr.c NetSutils.c NetSparms.c

UNIX and Win32 source code are identical except for end-of-line characters.

Help can be obtained by entering NetSearch from a command line without any parameters.


NetSearch programs

Copyright (c) 2002 by John Aach and the President and Fellows of Harvard University

All other material

Copyright (c) 2002 by Martin Steffen, Allegra Petti and the President and Fellows of Harvard University

Further Assistance

Contact Martin Steffen or Allegra Petti for further assistance.