title: Molecular profiling of thyroid cancer subtypes using large-scale text mining.
abstract: BACKGROUND
  Thyroid cancer is the most common endocrine tumor with a steady increase in incidence. It is classified into multiple histopathological subtypes with potentially distinct molecular mechanisms. Identifying the most relevant genes and biological pathways reported in the thyroid cancer literature is vital for understanding of the disease and developing targeted therapeutics.
  
  
  RESULTS
  We developed a large-scale text mining system to generate a molecular profiling of thyroid cancer subtypes. The system first uses a subtype classification method for the thyroid cancer literature, which employs a scoring scheme to assign different subtypes to articles. We evaluated the classification method on a gold standard derived from the PubMed Supplementary Concept annotations, achieving a micro-average F1-score of 85.9% for primary subtypes. We then used the subtype classification results to extract genes and pathways associated with different thyroid cancer subtypes and successfully unveiled important genes and pathways, including some instances that are missing from current manually annotated databases or most recent review articles.
  
  
  CONCLUSIONS
  Identification of key genes and pathways plays a central role in understanding the molecular biology of thyroid cancer. An integration of subtype context can allow prioritized screening for diagnostic biomarkers and novel molecular targeted therapeutics. Source code used for this study is made freely available online at https://github.com/chengkun-wu/GenesThyCan.
authors.forename: Chengkun
authors.initials: C
authors.lastname: Wu
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Schwartz
authors.forename: Georg
authors.initials: G
authors.lastname: Brabant
authors.forename: Goran
authors.initials: G
authors.lastname: Nenadic
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D013964:Thyroid Neoplasms / Q000145:classification* / Q000235:genetics