Optimal consistency in microRNA expression analysis using reference-gene-based normalization

Molecular BioSystems
Xi WangMurray J Cairns

Abstract

Normalization of high-throughput molecular expression profiles secures differential expression analysis between samples of different phenotypes or biological conditions, and facilitates comparison between experimental batches. While the same general principles apply to microRNA (miRNA) normalization, there is mounting evidence that global shifts in their expression patterns occur in specific circumstances, which pose a challenge for normalizing miRNA expression data. As an alternative to global normalization, which has the propensity to flatten large trends, normalization against constitutively expressed reference genes presents an advantage through their relative independence. Here we investigated the performance of reference-gene-based (RGB) normalization for differential miRNA expression analysis of microarray expression data, and compared the results with other normalization methods, including: quantile, variance stabilization, robust spline, simple scaling, rank invariant, and Loess regression. The comparative analyses were executed using miRNA expression in tissue samples derived from subjects with schizophrenia and non-psychiatric controls. We proposed a consistency criterion for evaluating methods by examining the overl...Continue Reading

References

Jan 1, 1997·Schizophrenia Bulletin·T M Hyde, D R Weinberger
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Jul 23, 2003·Bioinformatics·D L WilsonI W Wilson
Jan 7, 2004·Biochemical and Biophysical Research Communications·Aleksandar RadonićAndreas Nitsche
Feb 17, 2005·Genes & Development·Chryssa KanellopoulouKlaus Rajewsky
Jun 10, 2005·Nature·Jun LuTodd R Golub
Jun 10, 2005·Nature·S D HatfieldH Ruohola-Baker
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Aug 3, 2006·Genes & Development·J Michael ThomsonScott M Hammond
Jan 8, 2008·Nucleic Acids Research·Simon M LinWarren A Kibbe
May 10, 2008·Bioinformatics·Pan DuSimon M Lin
Jun 3, 2008·Genomics·You-Jia HuaHua-Sheng Xiao
Aug 5, 2008·Statistical Applications in Genetics and Molecular Biology·Youlan RaoJohn P Hagan
Oct 17, 2008·PloS One·Ming LuQinghua Cui
Jan 30, 2009·RNA·Sylvain PradervandKeith Harshman
Aug 1, 2009·Journal of Theoretical Biology·Yunfei PeiXuegong Zhang
Sep 2, 2009·Molecular Psychiatry·N J BeveridgeM J Cairns
Feb 17, 2010·Database : the Journal of Biological Databases and Curation·A LaganàA Ferro
May 18, 2010·BMC Bioinformatics·Inna ChervonevaTerry Hyslop
Jul 29, 2010·Journal of Translational Medicine·Yingdong ZhaoLisa M McShane
Dec 31, 2011·Neurobiology of Disease·Natalie J Beveridge, Murray J Cairns
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder
Sep 8, 2012·Cellular Oncology (Dordrecht)·Sadegh BabashahMasoud Soleimani
Jan 31, 2013·Journal of Molecular Cell Biology·Adam P CarrollMurray J Cairns
Feb 5, 2013·Neurobiology of Disease·Edgardo Rodriguez-LebronBeverly L Davidson
May 27, 2014·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Margherita GrassoMichela A Denti
Nov 6, 2014·Experimental and Therapeutic Medicine·Jie WangYuanshuai Huang

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Citations

Oct 16, 2015·Journal of Medicinal Chemistry·Melissa Coates Ford, P Shing Ho
Dec 31, 2014·The Journal of Physical Chemistry. a·Luis Miguel AzofraSteve Scheiner
May 20, 2017·Nucleic Acids Research·Bo LiFeng Zhu
Sep 27, 2015·Clinical Chemistry·Heidi SchwarzenbachKlaus Pantel
Jun 9, 2020·Briefings in Bioinformatics·Jing TangFeng Zhu

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