title: Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling.
abstract: Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and predicting outcome. However, identifying perturbed pathways is challenging, because different tumors can have the same perturbed pathways that are perturbed by different SGAs. Here, we designed novel semantic representations that capture the functional similarity of distinct SGAs perturbing a common pathway in different tumors. Combining this representation with topic modeling would allow us to identify patterns in altered signaling pathways.
  
  
  
  We represented each gene with a vector of words describing its function, and we represented the SGAs of a tumor as a text document by pooling the words representing individual SGAs. We applied the nested hierarchical Dirichlet process (nHDP) model to a collection of tumors of 5 cancer types from TCGA. We identified topics (consisting of co-occurring words) representing the common functional themes of different SGAs. Tumors were clustered based on their topic associations, such that each cluster consists of tumors sharing common functional themes. The resulting clusters contained mixtures of cancer types, which indicates that different cancer types can share disease mechanisms. Survival analysis based on the clusters revealed significant differences in survival among the tumors of the same cancer type that were assigned to different clusters.
  
  
  
  The results indicate that applying topic modeling to semantic representations of tumors identifies patterns in the combinations of altered functional pathways in cancer.
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 500, Pittsburgh, PA, 15206, USA.
authors.forename: Vicky
authors.initials: V
authors.lastname: Chen
authors.affiliation: Department of Electrical Engineering, Columbia University, 500 W. 120th St., Suite 1300, New York, NY, 10027, USA.
authors.forename: John
authors.initials: J
authors.lastname: Paisley
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 500, Pittsburgh, PA, 15206, USA. xinghua@pitt.edu.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Lu
mesh_terms: D016000:Cluster Analysis; D005260:Female; D006801:Humans; D051188:Knowledge Bases; D008297:Male; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism* / Q000401:mortality; D011379:Prognosis; D012660:Semantics; D016019:Survival Analysis
keywords: Cancer; Cancer genomics; Disease mechanisms; Semantic representation; Topic modeling