Abstract
BackgroundTraditional cancer treatments have centered on cytotoxic drugs and general purpose chemotherapy that may not be tailored to treat specific cancers. Identification of molecular markers that are related to different types of cancers might lead to discovery of drugs that are patient and disease specific. This study aims to use microarray gene expression cancer data to identify biomarkers that are indicative of different types of cancers. Our aim is to provide a multi-class cancer classifier that can simultaneously differentiate between cancers and identify type-specific biomarkers, through the application of the Binary Coded Genetic Algorithm (BCGA) and a neural network based Extreme Learning Machine (ELM) algorithm.ResultsBCGA and ELM are combined and used to select a subset of genes that are present in the Global Cancer Mapping (GCM) data set. This set of candidate genes contains over 52 biomarkers that are related to multiple cancers, according to the literature. They include APOA1, VEGFC, YWHAZ, B2M, EIF2S1, CCR9 and many other genes that have been associated with the hallmarks of cancer. BCGA-ELM is tested on several cancer data sets and the results are compared to other classification methods. BCGA-ELM compares or exceeds other algorithms in terms of accuracy. We were also able to show that over 50% of genes selected by BCGA-ELM on GCM data are cancer related biomarkers.ConclusionsWe were able to simultaneously differentiate between 14 different types of cancers, using only 92 genes, to achieve a multi-class classification accuracy of 95.4% which is between 21.6% and 38% higher than other results in the literature for multi-class cancer classification. Our findings suggest that computational algorithms such as BCGA-ELM can facilitate biomarker-driven integrated cancer research that can lead to a detailed understanding of the complexities of cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0565-5) contains supplementary material, which is available to authorized users.
Highlights
Traditional cancer treatments have centered on cytotoxic drugs and general purpose chemotherapy that may not be tailored to treat specific cancers
Discovery of biomarkers by Binary Coded Genetic Algorithm (BCGA)-Extreme Learning Machine (ELM) The BCGA-ELM algorithm selects the minimum set of 92 candidate features that have the best discriminatory power to differentiate between 14 types of cancers, with 95.4% accuracy
BCGA-ELM selects smaller sets of features, ranging between 11 and 73 genes, from 8 other cancer data sets which help to classify these cancers with high accuracy
Summary
Traditional cancer treatments have centered on cytotoxic drugs and general purpose chemotherapy that may not be tailored to treat specific cancers. Identification of molecular markers that are related to different types of cancers might lead to discovery of drugs that are patient and disease specific. This study aims to use microarray gene expression cancer data to identify biomarkers that are indicative of different types of cancers. Our aim is to provide a multi-class cancer classifier that can simultaneously differentiate between cancers and identify type-specific biomarkers, through the application of the Binary Coded Genetic Algorithm (BCGA) and a neural network based Extreme Learning Machine (ELM) algorithm. The application of computational methods to identify biomarkers that encode these cancer causing changes can Sachnev et al BMC Bioinformatics (2015) 16:166 provide clinicians with a valuable tool that could lead to advances in the understanding, treatment and prognosis for cancer. Other improved and efficient methods include genetic algorithm for gene selection combined with SVM and fuzzy neural networks [13,14]
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