title: Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung.
abstract: Lung cancer accounts for the most cancer-related deaths. The identification of cancer-associated genes and the related pathways are essential to prevent many types of cancer. In this paper, a more systematic approach is considered. First, we did pathway analysis using Hyper Geometric Distribution (HGD) and significantly overrepresented sets of reactions were identified. Second, feature-selection-based Particle Swarm Optimisation (PSO), Information Gain (IG) and the Biomarker Identifier (BMI) for the identification of different types of lung cancer were used. We also evaluated PSO and developed a new method to determine the BMI thresholds to prioritize genes. We were able to identify sets of key genes that can be found in several pathways. Experimental results show that our method simplifies features effectively and obtains higher classification accuracy than the other methods from the literature.
authors.affiliation: Bioinformatics Core Facility, University of Kansas Lawrence, KS 66047, USA. mvisvanathan@ku.edu
authors.forename: Mahesh
authors.initials: M
authors.lastname: Visvanathan
authors.forename: Michael
authors.initials: M
authors.lastname: Netzer
authors.forename: Michael
authors.initials: M
authors.lastname: Seger
authors.forename: Bhargav S
authors.initials: BS
authors.lastname: Adagarla
authors.forename: Christian
authors.initials: C
authors.lastname: Baumgartner
authors.forename: Sitta
authors.initials: S
authors.lastname: Sittampalam
authors.forename: Gerald H
authors.initials: GH
authors.lastname: Lushington
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D053858:Metabolic Networks and Pathways; D009857:Oncogenes; D013269:Stochastic Processes