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.
References: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