ICN: a normalization method for gene expression data considering the over-expression of informative genes
Publication in refereed journal


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摘要The global increase of gene expression has been frequently established in cancer microarray studies. However, many genes may not deliver informative signals for a given experiment, due to insufficient expression or even non-expression, despite the DNA microarrays massively measuring genes in parallel. Hence the informative gene set, rather than the whole genome, should be more reasonable to represent the genome expression level. We observed that the trend of over-expression for informative genes is more obvious in human cancers, which is to some extent masked using the whole genome without any filtering. Accordingly we proposed a novel normalization method, Informative CrossNorm (ICN), which performs the cross normalization (CrossNorm) on the expression matrix merely containing the informative genes. ICN outperforms other methods with a consistently high precision, F-score, and Matthews correlation coefficient as well as an acceptable recall based on three available spiked-in datasets with ground truth. In addition, nine potential therapeutic target genes for esophageal squamous cell carcinoma (ESCC) were identified using ICN integrated with a protein-protein interaction network, which biologically demonstrates that ICN shows superior performance. Consequently, it is expected that ICN could be applied routinely in cancer microarray studies.
著者Cheng LX, Wang X, Wong PK, Lee KY, Li L, Xu B, Wang D, Leung KS
期刊名稱Molecular BioSystems
出版年份2016
卷號12
期次10
出版社ROYAL SOC CHEMISTRY
頁次3057 - 3066
國際標準期刊號1742-206X
語言英式英語
Web of Science 學科類別Biochemistry & Molecular Biology

上次更新時間 2020-19-10 於 03:10