title: ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers.
abstract: BACKGROUND
  With the explosion of genomic data over the last decade, there has been a tremendous amount of effort to understand the molecular basis of cancer using informatics approaches. However, this has proven to be extremely difficult primarily because of the varied etiology and vast genetic heterogeneity of different cancers and even within the same cancer. One particularly challenging problem is to predict prognostic outcome of the disease for different patients.
  
  
  RESULTS
  Here, we present ENCAPP, an elastic-net-based approach that combines the reference human protein interactome network with gene expression data to accurately predict prognosis for different human cancers. Our method identifies functional modules that are differentially expressed between patients with good and bad prognosis and uses these to fit a regression model that can be used to predict prognosis for breast, colon, rectal, and ovarian cancers. Using this model, ENCAPP can also identify prognostic biomarkers with a high degree of confidence, which can be used to generate downstream mechanistic and therapeutic insights.
  
  
  CONCLUSIONS
  ENCAPP is a robust method that can accurately predict prognostic outcome and identify biomarkers for different human cancers.
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, 335 Weill Hall, Ithaca, NY, 14853, USA. jd327@cornell.edu.|Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA. jd327@cornell.edu.
authors.forename: Jishnu
authors.initials: J
authors.lastname: Das
authors.affiliation: Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA. kmg257@cornell.edu.
authors.forename: Kaitlyn M
authors.initials: KM
authors.lastname: Gayvert
authors.affiliation: Department of Statistical Science, Cornell University, Ithaca, NY, 14853, USA. fb238@cornell.edu.
authors.forename: Florentina
authors.initials: F
authors.lastname: Bunea
authors.affiliation: Department of Statistical Science, Cornell University, Ithaca, NY, 14853, USA. marten.wegkamp@cornell.edu.
authors.forename: Marten H
authors.initials: MH
authors.lastname: Wegkamp
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, 335 Weill Hall, Ithaca, NY, 14853, USA. haiyuan.yu@cornell.edu.|Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA. haiyuan.yu@cornell.edu.
authors.forename: Haiyuan
authors.initials: H
authors.lastname: Yu
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism*; D019295:Computational Biology; D015870:Gene Expression; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000378:metabolism*; D011379:Prognosis; D060066:Protein Interaction Maps; D012984:Software
chemical_list: D014408:Biomarkers, Tumor