Analysis Tools


Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

EMAP Toolbox

EMAP Toolbox is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.


MiST: Mass Spectrometry interaction STatistics is a computational tool for scoring of affinity purification-mass spectrometry data. We have also developed a stand-alone version of MiST in R.

Citation: Jäger et al. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21;481(7381):365-70. PMCID: PMC3310911

Network-Based Stratification

image10The Ideker group recently introduced the method of Network-Based Stratification (NBS), which allows for stratification of cancer into informative subtypes by clustering together patients who have somatic mutations that impact common regions of a reference molecular interaction network. NBS has been applied to ovarian, uterine, and lung cancer and, more recently, thyroid cancer cohorts. For each of these cancer types, NBS identified clear subtypes predictive of clinical outcomes such as patient survival or response to therapy, and it identified network regions characteristic of each subtype.

Citation: Hofree et al. Network-based stratification of tumor mutations. Nat Methods. 2013 Nov; 10(11): 1108–1115. PMCID: PMC3866081