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:

HTTP://WWW.MAAYANLAB.NET/X2K

A web-based version of Genes2Networks with a GUI interface is also available from here:
http://actin.pharm.mssm.edu/genes2networks

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_Win.zip

Genes2Networks_Lnx.zip

Genes2Networks_Mac.zip

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

SAVI.sig

6/1/2006

16099987

HPRD

http://www.hprd.org

HPRD.sig*

7/25/2006

14525934

BIND

http://bind.ca

BIND.sig**

2/24/2006

11125103

MINT

http://mint.bio.uniroma2.it/

MINT.sig

9/25/2006

17135203

DIP

http://dip.doe-mbi.ucla.edu/

DIP.sig**

9/25/2006

10592249

IntAct

http://www.ebi.ac.uk/intact/site/index.jsf

IntAct.sig

9/25/2006

17145710

PPID

http://www.anc.ed.ac.uk/mscs/PPID/

PPID.sig**

12/3/2003

N/A

PDZBase

http://icb.med.cornell.edu/services/pdz/start

PDZBase.sig

2/15/2005

15513994

Vidal

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16189514

vidal.sig

9/25/2006

16189514

Stelzl

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16169070

stelzl.sig

9/25/2006

16169070

* These files are not available in SIG format but can be created using the tools listed in the table above.
** These files were created using other scripts and are only available upon request internally to Mount Sinai researchers due to licensing restrictions.

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