Testing for differentially-expressed microRNAs with errors-in-variables nonparametric regression.
MicroRNA is a set of small RNA molecules mediating gene expression at post-transcriptional/translational levels. Most of well-established high throughput discovery platforms, such as microarray, real time quantitative PCR, and sequencing, have been adapted to study microRNA in various human diseases. The total number of microRNAs in humans is approximately 1,800, which challenges some analytical methodologies requiring a large number of entries. Unlike messenger RNA, the majority of microRNA (>60%) maintains relatively low abundance in the cells. When analyzed using microarray, the signals of these low-expressed microRNAs are influenced by other non-specific signals including the background noise. It is crucial to distinguish the true microRNA signals from measurement errors in microRNA array data analysis. In this study, we propose a novel measurement error model-based normalization method and differentially-expressed microRNA detection method for microRNA profiling data acquired from locked nucleic acids (LNA) microRNA array. Compared with some existing methods, the proposed method significantly improves the detection among low-expressed microRNAs when assessed by quantitative real-time PCR assay.
Mathematics and Statistics Department, University of South Alabama, Mobile, Alabama, United States of America. bwang@jaguar1.usouthal.edu
Bin
B
Wang
Shu-Guang
SG
Zhang
Xiao-Feng
XF
Wang
Ming
M
Tan
Yaguang
Y
Xi
D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics*; D012044:Regression Analysis; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D035683:MicroRNAs; D009841:Oligonucleotides; C477371:locked nucleic acid