Artificial neural networks and decision tree model analysis of liver cancer proteomes

Biochem Biophys Res Commun. 2007 Sep 14;361(1):68-73. doi: 10.1016/j.bbrc.2007.06.172. Epub 2007 Jul 10.


Hepatocellular carcinoma (HCC) is a heterogeneous cancer and usually diagnosed at late advanced tumor stages of high lethality. The present study attempted to obtain a proteome-wide analysis of HCC in comparison with adjacent non-tumor liver tissues, in order to facilitate biomarkers' discovery and to investigate the mechanisms of HCC development. A cohort of 66 Chinese patients with HCC was included for proteomic profiling study by two-dimensional gel electrophoresis (2-DE) analysis. Artificial neural network (ANN) and decision tree (CART) data-mining methods were employed to analyze the profiling data and to delineate significant patterns and trends for discriminating HCC from non-malignant liver tissues. Protein markers were identified by tandem MS/MS. A total of 132 proteome datasets were generated by 2-DE expression profiling analysis, and each with 230 consolidated protein expression intensities. Both the data-mining algorithms successfully distinguished the HCC phenotype from other non-malignant liver samples. The detection sensitivity and specificity of ANN were 96.97% and 87.88%, while those of CART were 81.82% and 78.79%, respectively. The three biological classifiers in the CART model were identified as cytochrome b5, heat shock 70 kDa protein 8 isoform 2, and cathepsin B. The 2-DE-based proteomic profiling approach combined with the ANN or CART algorithm yielded satisfactory performance on identifying HCC and revealed potential candidate cancer biomarkers.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Biomarkers, Tumor / analysis*
  • Biomarkers, Tumor / classification
  • Carcinoma, Hepatocellular / diagnosis*
  • Decision Trees*
  • Electrophoresis, Gel, Two-Dimensional
  • Female
  • Humans
  • Liver
  • Liver Neoplasms / diagnosis*
  • Male
  • Middle Aged
  • Neoplasm Proteins / analysis*
  • Neoplasm Proteins / classification
  • Neural Networks, Computer*
  • Proteome / chemistry
  • Proteomics / methods*
  • Tandem Mass Spectrometry


  • Biomarkers, Tumor
  • Neoplasm Proteins
  • Proteome