Genes2Networks- Command-line Version (old implemetation)
A newer version of Genes2Networks is available with the Expression2Kinases application. This version contains an updated database of protein-protein interactions and more network visualization options: Genes2Networks is a command-line software tool
that can be used to place lists of mammalian genes in the context of a
background mammalian signalome and interactome networks. The input to the program is a list of
human Entrez Gene gene symbols and background
networks in SIG
format, while the output includes: (a) all identified interactions for the genes/proteins,
(b) a subnetwork connecting the genes/proteins using
intermediate components that are used to connect the genes, (c) ranking of the
specificity of intermediate components to interact with the list of genes/proteins,
and (d) a clustering analysis of the genes/proteins from the seed list based on
their distance from one another in network space. Genes2Networks can be run on Linux, Mac and
Windows operating systems and it requires background network text files in SIG
format. Windows PC users can use the self-extracting
executable Genes2Networks_install.zip
to install the program. Mac and Linux users can use the command-line executables
listed in the table below: Windows Linux Mac Genes2Networks.exe Genes2Networks Genes2Networks HPRD2Sig.exe IntAct2Sig.exe
MINT2Sig.exe HPRD2Sig IntAct2Sig MINT2Sig HPRD2Sig IntAct2Sig MINT2Sig SwissProtUpdate.exe SwissProtUpdate SwissProtUpdate Genes2Networks requires network datasets in text file format representing
interaction networks to run properly. Several such datasets are provided in
table below and are available with the downloadable programs: Name URL SIG file Date created PMID CA1 Neuron http://www.mssm.edu/labs/maayan/resources/datasets/qualitative_networks.shtml 6/1/2006 16099987 HPRD HPRD.sig* 7/25/2006 14525934 BIND BIND.sig** 2/24/2006 11125103 MINT 9/25/2006 17135203 DIP DIP.sig** 9/25/2006 10592249 IntAct 9/25/2006 17145710 PPID PPID.sig** 12/3/2003 N/A PDZBase 2/15/2005 15513994 Vidal 9/25/2006 16189514 Stelzl 9/25/2006 16169070 * These files are not available in SIG format but can be created using the
tools listed in the table above.
The rest of the SIG files are provided with the downloadable compressed
files. To run Genes2Networks, list any number of networks (SIG
files) at the command line after the Genes2Networks executable. For example: genes2networks.exe BIND.sig MINT.sig IntAct.sig Then press enter and follow the instructions as illustrated below: Steps: The program searches for paths from all pairs of genes/proteins from the seed
list by attempting to connect those genes/proteins using the background
networks. The following is a screen shot of where you specify the number of
intermediates to use to connect the genes/proteins from the seed list. If you want to find ONLY interactions between the nodes in the list enter 1. To use ONE intermediate connect the genes/proteins from the seed list enter
the number 2 (which is recommended and illustrated above). Filtering: Genes2Networks provides two types of filtering methods:
a.remove articles that contribute to too many interactions b.remove interactions with few references The recommended selection is to filter out articles that contribute to too
many interactions with a threshold set to between 3 and 8. A screen shot for selecting such settings is shown below: The list of genes: Users should enter lists of genes as either a text file (the text file
should contain one column listing the gene names, and the text file’s name should
be typed on the command line), or, alternatively, type in the gene names one by
one as shown below. To exit this section type in a period (.) and press enter. An example of creating a subnetwork connecting
EGFR, MAPK3 and SOS1 is shown below: Only human genes names should be used. To find the unambiguous gene symbol
for a specific protein use Entrez Gene. The final outputs are a SIG file and a SIF file. To specify the name of these
files type a unique name on the command line without any file extension as
shown below: The output SIG and SIF files will be present in your current working
directory: These files can be analyzed and visualized using SNAVI for
SIG files and/or Cytoscape
for SIF files. The source code for Genes2Networks and the tools
to convert existing protein and signaling interaction network databases into
the SIG format will be provided on this site soon. The use of the data and programs available on
this site is for academic users only, commercial users should contact technology@mssm.edu. For assistance e-mail questions to avi.maayan@mssm.edu
A web-based version of Genes2Networks with a GUI interface is also available from here:
http://actin.pharm.mssm.edu/genes2networks
** These files were created using other scripts and are only available upon
request internally to Mount Sinai researchers due
to licensing restrictions.
