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Three microarray platforms: an analysis of their concordance in profiling gene expression.

Petersen D, Chandramouli GV, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barrett JC, Green J, Kawasaki ES - BMC Genomics (2005)

Bottom Line: When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%.Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties.All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.

View Article: PubMed Central - HTML - PubMed

Affiliation: Advanced Technology Center, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD 20877, USA. petersed@mail.nih.gov

ABSTRACT

Background: Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25-30 base), long oligonucleotide (50-80 base), and cDNA (highly variable in length). The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date, but long oligonucleotide platforms are gaining in popularity and will probably replace cDNA arrays. As part of a validation study for the long oligonucleotide arrays, we compared and contrasted expression profiles from the three formats, testing RNA from six different cell lines against a universal reference standard.

Results: The three platforms had 6430 genes in common. In general, correlation of gene expression levels across the platforms was good when defined by concordance in the direction of expression difference (upregulation or downregulation), scatter plot analysis, principal component analysis, cell line correlation or quantitative RT-PCR. The overall correlations (r values) between platforms were in the range 0.7 to 0.8, as determined by analysis of scatter plots. When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%.

Conclusion: Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties. All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.

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a-f. Scatter plot analysis to determine correlation coefficients between and within platforms using Jurkat RNA as an example. Correlations for all cell lines are given in Table 4. (a) Operon versus Incyte (b) Affymetrix versus Incyte (c) Affymetrix versus Operon (d) GEM2 versus GEM2 replicate correlation (e) Operon versus Operon (f) HG-U133A versus HG-U133A
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Figure 2: a-f. Scatter plot analysis to determine correlation coefficients between and within platforms using Jurkat RNA as an example. Correlations for all cell lines are given in Table 4. (a) Operon versus Incyte (b) Affymetrix versus Incyte (c) Affymetrix versus Operon (d) GEM2 versus GEM2 replicate correlation (e) Operon versus Operon (f) HG-U133A versus HG-U133A

Mentions: The scatter plots shown in Figures 2a–c indicate graphically the correlation between the platforms for Jurkat RNA. Values of r for all platforms and all cell lines are given in Table 4. The values ranged from 0.7 to 0.8. Operon and Affymetrix were better correlated than were Operon and Incyte. The values were intermediate for the relationship between Incyte and Affymetrix. Figures 2d–f and Table 5 indicate that the correlation coefficients between replicates within the same platform are closer, as expected, when compared to the correlations between platforms. In general, however, there was reasonably good concordance among the platforms.


Three microarray platforms: an analysis of their concordance in profiling gene expression.

Petersen D, Chandramouli GV, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barrett JC, Green J, Kawasaki ES - BMC Genomics (2005)

a-f. Scatter plot analysis to determine correlation coefficients between and within platforms using Jurkat RNA as an example. Correlations for all cell lines are given in Table 4. (a) Operon versus Incyte (b) Affymetrix versus Incyte (c) Affymetrix versus Operon (d) GEM2 versus GEM2 replicate correlation (e) Operon versus Operon (f) HG-U133A versus HG-U133A
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1140753&req=5

Figure 2: a-f. Scatter plot analysis to determine correlation coefficients between and within platforms using Jurkat RNA as an example. Correlations for all cell lines are given in Table 4. (a) Operon versus Incyte (b) Affymetrix versus Incyte (c) Affymetrix versus Operon (d) GEM2 versus GEM2 replicate correlation (e) Operon versus Operon (f) HG-U133A versus HG-U133A
Mentions: The scatter plots shown in Figures 2a–c indicate graphically the correlation between the platforms for Jurkat RNA. Values of r for all platforms and all cell lines are given in Table 4. The values ranged from 0.7 to 0.8. Operon and Affymetrix were better correlated than were Operon and Incyte. The values were intermediate for the relationship between Incyte and Affymetrix. Figures 2d–f and Table 5 indicate that the correlation coefficients between replicates within the same platform are closer, as expected, when compared to the correlations between platforms. In general, however, there was reasonably good concordance among the platforms.

Bottom Line: When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%.Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties.All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.

View Article: PubMed Central - HTML - PubMed

Affiliation: Advanced Technology Center, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD 20877, USA. petersed@mail.nih.gov

ABSTRACT

Background: Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25-30 base), long oligonucleotide (50-80 base), and cDNA (highly variable in length). The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date, but long oligonucleotide platforms are gaining in popularity and will probably replace cDNA arrays. As part of a validation study for the long oligonucleotide arrays, we compared and contrasted expression profiles from the three formats, testing RNA from six different cell lines against a universal reference standard.

Results: The three platforms had 6430 genes in common. In general, correlation of gene expression levels across the platforms was good when defined by concordance in the direction of expression difference (upregulation or downregulation), scatter plot analysis, principal component analysis, cell line correlation or quantitative RT-PCR. The overall correlations (r values) between platforms were in the range 0.7 to 0.8, as determined by analysis of scatter plots. When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%.

Conclusion: Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties. All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.

Show MeSH