Welcome to OmicsIntegrator

Forest takes protein data, maps it onto a large interactome network, and then uses the Prize-Collecting Steiner Forest algorithm to identify a high-confidence subnetwork relevant to your data. This can help identify cellular pathways and other proteins that are involved in your experimental system.

Sample files: Sample prize file · Sample interactome file


Upload your high-throughput data below. The file should be tab-delimited, with the first two required columns "name" and "prize". Following columns may include other information about your molecules, such as "type" to indicate what high-throughput assay implicated that molecule (i.e. "protein" for a proteomic screen, or "TF" for Garnet results). For an example prize file, see the sample data above.

Upload prize file
If you are using the default interactome, prize nodes should be indicated by Gene Symbols.

Interactome/Edge file

Optional: Upload your own Interactome (edge) file

If left blank the iRefIndex v14 interactome will be used.
Note that with the latest version of Omics Integrator, edges with higher costs are less likely to be chosen in the solution. If you use the default interactome, this change has been addressed for you.

Algorithm Parameters

Dummy Edge Weight (w):
Edge Reliability (b):
Degree Penalty (g):
Randomize Prizes (# of runs):


Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. N Tuncbag, SJC Gosline, AJ Kedaigle, AR Soltis, A Gitter, E Fraenkel. PLoS Computational Biology, 2016; 12(4).

For more advanced control over your run, and to use the Garnet tool, you can run Omics Integrator on your own computer.

Version 1: https://github.com/fraenkel-lab/OmicsIntegrator
Protocol paper for version 1: Discovering altered regulation and signaling through network-based integration of transcriptomic, epigenomic and proteomic tumor data. Kedaigle A, and Fraenkel E. Cancer Systems Biology: Methods in Molecular Biology, 2018.

Version 2: https://github.com/fraenkel-lab/OmicsIntegrator2

This website is free for academic purposes.