Semi-supervised methods to predict patient survival from gene expression data

PLoS Biol. 2004 Apr;2(4):E108. doi: 10.1371/journal.pbio.0020108. Epub 2004 Apr 13.


An important goal of DNA microarray research is to develop tools to diagnose cancer more accurately based on the genetic profile of a tumor. There are several existing techniques in the literature for performing this type of diagnosis. Unfortunately, most of these techniques assume that different subtypes of cancer are already known to exist. Their utility is limited when such subtypes have not been previously identified. Although methods for identifying such subtypes exist, these methods do not work well for all datasets. It would be desirable to develop a procedure to find such subtypes that is applicable in a wide variety of circumstances. Even if no information is known about possible subtypes of a certain form of cancer, clinical information about the patients, such as their survival time, is often available. In this study, we develop some procedures that utilize both the gene expression data and the clinical data to identify subtypes of cancer and use this knowledge to diagnose future patients. These procedures were successfully applied to several publicly available datasets. We present diagnostic procedures that accurately predict the survival of future patients based on the gene expression profile and survival times of previous patients. This has the potential to be a powerful tool for diagnosing and treating cancer.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Breast Neoplasms / metabolism
  • Breast Neoplasms / mortality
  • Cluster Analysis
  • Computer Simulation
  • Data Interpretation, Statistical
  • Databases, Factual
  • Gene Expression Profiling*
  • Humans
  • Models, Statistical
  • Neoplasms / metabolism*
  • Neoplasms / mortality*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Principal Component Analysis
  • Prognosis
  • Software
  • Time Factors
  • Treatment Outcome