* 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 SAVI 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
