Entropy-based analysis of the non-linear relationship between gene expression profiles of amplified and non-amplified RNA.
Two critical issues in microarray-based gene expression profiling with amplified RNA are its reliability and reproducibility compared to the non-amplified RNA. In this study, the non-linear relationship between the two methods was evaluated with the entropy in addition to the linear relationship using correlation coefficients. The correlation coefficients within the amplification method and between the two methods were significantly high, 0.98 and 0.88, respectively. Comparing the entropy as increasing fold-change difference (k), the average entropy value was reduced to 0.02 in the cell line and 0.09 in the tissue samples, indicating that the number of different genes between the two methods was decreased. In addition, the threshold of k according to the percentage of p estimated from entropy values could be used to provide the cut-off line on gene selection. The quantity discordance rate of 0.3-5.47% and the common outlier proportion of 84.2-94.3% between the two methods were detected, according to the expression levels. In summary, we showed a high similarity between the two methods using non-linear as well as linear comparison. Furthermore, we proved that the entropy as the measure of non-linear relationship is useful for analyzing the similarity of replicated microarray data sets.
Shin
Ji Hye
JH
Cancer Metastasis Research Center, Yonsei University College of Medicine, Shinchon-Dong, Seoul, Korea.
Park
Chan Ho
CH
Yang
Yeon Ju
YJ
Kim
Sang Chul
SC
Seo
Min Young
MY
Yang
Sang Hwa
SH
Cho
Sung Bae
SB
Chung
Hyun Cheol
HC
Rha
Sun Young
SY
D045744:Cell Line, Tumor; D019277:Entropy; D020869:Gene Expression Profiling; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D013223:Statistics as Topic
D012313:RNA