A filter-based feature selection approach for identifying potential biomarkers for lung cancer

Abstract

Background: Lung cancer is the leading cause of death from cancer in the world and its treatment is dependant on the type and stage of cancer detected in the patient. Molecular biomarkers that can characterize the cancer phenotype are thus a key tool in planning a therapeutic response. A common protocol for identifying such biomarkers is to employ genomic microarray analysis to find genes that show differential expression according to disease state or type. Data-mining techniques such as feature selection are often used to isolate, from among a large manifold of genes with differential expression, those specific genes whose differential expression patterns are of optimal value in phenotypic differentiation. One such technique, Biomarker Identifier (BMI), has been developed to identify features with the ability to distinguish between two data groups of interest, which is thus highly applicable for such studies.

Results: Microarray data with validated genes was used to evaluate the utility of BMI in identifying markers for lung cancer. This data set contains a set of 129 gene expression profiles from large-airway epithelial cells (60 samples from smokers with lung cancer and 69 from smokers without lung cancer) and 7 genes from this data have been confirmed to be differentially expressed by quantitative PCR. Using this data set, BMI was compared with various well-known feature selection methods and was found to be more successful than other methods in finding useful genes to classify cancerous samples. Also it is evident that genes selected by BMI (given the same number of genes and classification algorithms) showed better discriminative power than those from the original study. After pathway analysis on the selected genes by BMI, we have been able to correlate the selected genes with well-known cancer-related pathways.

Conclusions: Our results show that BMI can be used to analyze microarray data and to find useful genes for classifying samples. Pathway analysis suggests that BMI is successful in identifying biomarker-quality cancer-related genes from the data.

Figure 1

The median ranks of validated genes in airway data set by various feature selection methods.