Improved Classification of Lung Cancer Tumors Based on Structural and Physicochemical Properties of Proteins Using Data Mining Models

• Published in: PloS one Vol. 8; no. 3; p. e58772
• Main Authors: Ramani, R. Geetha, Jacob, Shomona Gracia
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 07.03.2013; Public Library of Science (PLoS)
• Subjects: Accuracy; Algorithms; Analysis; Artificial intelligence; Bayes Theorem; Bayesian analysis; Bioinformatics; Biology; Biomarkers; Cancer; Carcinoma, Non-Small-Cell Lung - classification; Classification; Cleaning; Cluster Analysis; Clustering; Computer applications; Computer Science; Data mining; Data Mining - methods; Data processing; Databases, Genetic; Diagnosis; Discriminant analysis; Divergence; DNA methylation; DNA microarrays; Drug development; Gene expression; Gene sequencing; Genes; Genetic counseling; Genomics; Health aspects; Humans; Hydrophobicity; Lung cancer; Lung diseases; Lung Neoplasms - classification; Mathematical models; Medical Informatics - methods; Medicine; Non-small cell lung cancer; Non-small cell lung carcinoma; Physicochemical properties; Polarizability; Properties (attributes); Protein composition; Proteins; Proteins - chemistry; Reproducibility of Results; Tumors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0058772

Detecting divergence between oncogenic tumors plays a pivotal role in cancer diagnosis and therapy. This research work was focused on designing a computational strategy to predict the class of lung cancer tumors from the structural and physicochemical properties (1497 attributes) of protein sequences obtained from genes defined by microarray analysis. The proposed methodology involved the use of hybrid feature selection techniques (gain ratio and correlation based subset evaluators with Incremental Feature Selection) followed by Bayesian Network prediction to discriminate lung cancer tumors as Small Cell Lung Cancer (SCLC), Non-Small Cell Lung Cancer (NSCLC) and the COMMON classes. Moreover, this methodology eliminated the need for extensive data cleansing strategies on the protein properties and revealed the optimal and minimal set of features that contributed to lung cancer tumor classification with an improved accuracy compared to previous work. We also attempted to predict via supervised clustering the possible clusters in the lung tumor data. Our results revealed that supervised clustering algorithms exhibited poor performance in differentiating the lung tumor classes. Hybrid feature selection identified the distribution of solvent accessibility, polarizability and hydrophobicity as the highest ranked features with Incremental feature selection and Bayesian Network prediction generating the optimal Jack-knife cross validation accuracy of 87.6%. Precise categorization of oncogenic genes causing SCLC and NSCLC based on the structural and physicochemical properties of their protein sequences is expected to unravel the functionality of proteins that are essential in maintaining the genomic integrity of a cell and also act as an informative source for drug design, targeting essential protein properties and their composition that are found to exist in lung cancer tumors.