Identification of Gene Signatures Used to Recognize Biological Characteristics of Gastric Cancer Upon Gene Expression Data

High-throughput gene expression microarrays can be examined by machine-learning algorithms to identify gene signatures that recognize the biological characteristics of specific human diseases, including cancer, with high sensitivity and specificity. A previous study compared 20 gastric cancer (GC) s...

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Bibliographic Details
Published in:Biomarker Insights 2014-01, Vol.2014 (9), p.67-76
Main Authors: Yan, Zhi, Luke, Brian T., Tsang, Shirley X., Xing, Rui, Pan, Yuanming, Liu, Yixuan, Wang, Jinlian, Geng, Tao, Li, Jiangeng, Lu, Youyong
Format: Article
Language:English
Subjects:
Algorithms
Cancer
Comparative analysis
Criminal investigation
Data mining
Gene expression
Genes
Genetic aspects
Immunohistochemistry
Machine learning
Original Research
Stomach cancer
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Summary:High-throughput gene expression microarrays can be examined by machine-learning algorithms to identify gene signatures that recognize the biological characteristics of specific human diseases, including cancer, with high sensitivity and specificity. A previous study compared 20 gastric cancer (GC) samples against 20 normal tissue (NT) samples and identified 1,519 differentially expressed genes (DEGs). In this study, Classification Information Index (CII), Information Gain Index (IGI), and RELIEF algorithms are used to mine the previously reported gene expression profiling data. In all, 29 of these genes are identified by all three algorithms and are treated as GC candidate biomarkers. Three biomarkers, COL1A2, ATP4B, and HADHSC, are selected and further examined using quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) staining in two independent sets of GC and normal adjacent tissue (NAT) samples. Our study shows that COL1A2 and HADHSC are the two best biomarkers from the microarray data, distinguishing all GC from the NT, whereas ATP4B is diagnostically significant in lab tests because of its wider range of fold-changes in expression. Herein, a data-mining model applicable for small sample sizes is presented and discussed. Our result suggested that this mining model may be useful in small sample-size studies to identify putative biomarkers and potential biological features of GC.
ISSN:1177-2719
1177-2719
DOI:10.4137/BMI.S13059