Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays.
As the data generated by microarray technology continue to amass, it is necessary to compare and combine gene expression data from different platforms. To evaluate the performance of cDNA and long oligonucleotide (60-mer) arrays, we generated gene expression profiles for two cancer cell lines and compared the data between the two platforms. All 6182 unique genes represented on both platforms were included in the analysis. A limited correlation (r = 0.4708) was obtained and the difference in measurement of low-expression genes was considered to contribute to the limited correlation. Further restriction of the data set to differentially expressed genes detected in cDNA microarrays (1205 genes) and oligonucleotide arrays (1325 genes) showed modest correlations of 0.7076 and 0.6441 between the two platforms. Quantitative real-time PCR measurements of a set of 10 genes showed better correlation with oligonucleotide arrays. Our results demonstrate that there is substantial variation in the data generated from cDNA and 60-mer oligonucleotide arrays. Although general agreement was observed in measurements of differentially expressed genes, we suggest that data from different platforms could not be directly amassed.
Zhu
Bingmei
B
Department of Molecular and Pharmaceutical Biotechnology, Graduate School of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan. bingmeizhu@yahoo.co.jp
Ping
Guichen
G
Shinohara
Yasuo
Y
Zhang
Yong
Y
Baba
Yoshinobu
Y
D045744:Cell Line, Tumor; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000502:physiology; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015345:Oligonucleotide Probes / Q000737:chemistry*; D011237:Predictive Value of Tests; D012680:Sensitivity and Specificity
D015345:Oligonucleotide Probes