Deciphering global signal features of high-throughput array data from cancers.
Normalization of array data relies on the assumption that most genes are not altered, which means that the signals for different samples should be scaled to have similar median or average values. However, accumulating evidence suggests that gene expression could be widely up-regulated in cancers. Our previous results and subsequent findings have shown that violation of the assumption led to erroneous interpretation of microarray data. To decipher the global signal features of microarray data from cancer samples, we empirically evaluated a large collection of gene and miRNA expression profiles and copy-number variation arrays. Our results showed that, at the transcriptomic level, genes and miRNAs are widely over-expressed in a large proportion of cancers. In contrast, at the genomic level, global raw signal intensities for methylation and copy number variation show negligible differences between cancer and normal samples. These results force us to re-evaluate the proper use of normalization procedures under different experimental conditions and for different array platforms.
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China. wangdong@ems.hrbmu.edu.cn lixia@hrbmu.edu.cn guoz@ems.hrbmu.edu.cn.
Deng
D
Wu
Juanjuan
J
Kang
Yan
Y
Huang
Xiang
X
Li
Xiansong
X
Wang
Dan
D
Huang
Yuting
Y
Wang
Bin
B
Li
Dapeng
D
Hao
Qi
Q
Gu
Nelson
N
Tang
Kongning
K
Li
Zheng
Z
Guo
Xia
X
Li
Jianzhen
J
Xu
Dong
D
Wang
D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D035683:MicroRNAs / Q000032:analysis; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis
D035683:MicroRNAs; D012333:RNA, Messenger