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

Abstract

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.

• Authors: John M Luk, Brian Y Lam, Nikki P Y Lee, David W Ho, Pak C Sham, Lei Chen, Jirun Peng, Xisheng Leng, Philip J Day, Sheung-Tat Fan
• Journal: Biochemical and biophysical research communications (Biochem Biophys Res Commun) Vol. 361 Issue 1 Pg. 68-73 (Sep 14 2007) ISSN: 0006-291X [Print] United States
• PMID: 17644064 (Publication Type: Comparative Study, Evaluation Study, Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• Biomarkers, Tumor
• Neoplasm Proteins
• Proteome

Topics

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