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

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

    Research output: Contribution to journalArticlepeer-review


    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. © 2007 Elsevier Inc. All rights reserved.
    Original languageEnglish
    Pages (from-to)68-73
    Number of pages5
    JournalBiochemical and Biophysical Research Communications
    Issue number1
    Publication statusPublished - 14 Sept 2007


    • ANN
    • Cancer proteome
    • CART
    • Classification
    • Hepatocellular carcinoma


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