Dysfunctions associated with methylation, microRNA expression and gene expression in lung cancer.
Integrating high-throughput data obtained from different molecular levels is essential for understanding the mechanisms of complex diseases such as cancer. In this study, we integrated the methylation, microRNA and mRNA data from lung cancer tissues and normal lung tissues using functional gene sets. For each Gene Ontology (GO) term, three sets were defined: the methylation set, the microRNA set and the mRNA set. The discriminating ability of each gene set was represented by the Matthews correlation coefficient (MCC), as evaluated by leave-one-out cross-validation (LOOCV). Next, the MCCs in the methylation sets, the microRNA sets and the mRNA sets were ranked. By comparing the MCC ranks of methylation, microRNA and mRNA for each GO term, we classified the GO sets into six groups and identified the dysfunctional methylation, microRNA and mRNA gene sets in lung cancer. Our results provide a systematic view of the functional alterations during tumorigenesis that may help to elucidate the mechanisms of lung cancer and lead to improved treatments for patients.
Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China.
Tao
T
Huang
Min
M
Jiang
Xiangyin
X
Kong
Yu-Dong
YD
Cai
D000368:Aged; D016000:Cluster Analysis; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology / Q000503:physiopathology; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D008875:Middle Aged; D011379:Prognosis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
D035683:MicroRNAs; D012333:RNA, Messenger