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Entropy-based analysis of the non-linear relationship between gene expression profiles of amplified and non-amplified RNA

Authors
 Ji Hye Shin  ;  Chan Ho Park  ;  Sun Young Rha  ;  Hyun Cheol Chung  ;  Sung Bae Cho  ;  Sang Hwa Yang  ;  Min Young Seo  ;  Sang Chul Kim  ;  Yeon Ju Yang 
Citation
 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, Vol.20(6) : 905-912, 2007 
Journal Title
 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 
ISSN
 1107-3756 
Issue Date
2007
MeSH
Cell Line, Tumor ; Entropy* ; Gene Expression Profiling* ; Humans ; Nucleic Acid Amplification Techniques ; Oligonucleotide Array Sequence Analysis ; RNA*/genetics ; RNA*/metabolism ; Reproducibility of Results ; Statistics as Topic*
Keywords
entropy ; non-linear relationship ; cDNA microarray ; RNA amplification
Abstract
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.
Full Text
http://www.spandidos-publications.com/ijmm/20/6/905
DOI
10.3892/ijmm.20.6.905
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
5. Research Institutes (연구소) > Cancer Metastasis Research Center (암전이연구센터) > 1. Journal Papers
Yonsei Authors
Rha, Sun Young(라선영) ORCID logo https://orcid.org/0000-0002-2512-4531
Yang, Sang Hwa(양상화)
Chung, Hyun Cheol(정현철) ORCID logo https://orcid.org/0000-0002-0920-9471
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/96180
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