Three microarray platforms: an analysis of their concordance in profiling gene expression
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2005-05-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/6/63 |
| _version_ | 1819180420630052864 |
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| author | Petersen David Chandramouli GVR Geoghegan Joel Hilburn Joanne Paarlberg Jonathon Kim Chang Munroe David Gangi Lisa Han Jing Puri Raj Staudt Lou Weinstein John Barrett J Carl Green Jeffrey Kawasaki Ernest S |
| author_facet | Petersen David Chandramouli GVR Geoghegan Joel Hilburn Joanne Paarlberg Jonathon Kim Chang Munroe David Gangi Lisa Han Jing Puri Raj Staudt Lou Weinstein John Barrett J Carl Green Jeffrey Kawasaki Ernest S |
| author_sort | Petersen David |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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%.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-22T22:14:04Z |
| format | Article |
| id | doaj.art-808a080004384952af4c7b500d3eb85c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T22:14:04Z |
| publishDate | 2005-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-808a080004384952af4c7b500d3eb85c2022-12-21T18:10:48ZengBMCBMC Genomics1471-21642005-05-01616310.1186/1471-2164-6-63Three microarray platforms: an analysis of their concordance in profiling gene expressionPetersen DavidChandramouli GVRGeoghegan JoelHilburn JoannePaarlberg JonathonKim ChangMunroe DavidGangi LisaHan JingPuri RajStaudt LouWeinstein JohnBarrett J CarlGreen JeffreyKawasaki Ernest S<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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%.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/6/63 |
| spellingShingle | Petersen David Chandramouli GVR Geoghegan Joel Hilburn Joanne Paarlberg Jonathon Kim Chang Munroe David Gangi Lisa Han Jing Puri Raj Staudt Lou Weinstein John Barrett J Carl Green Jeffrey Kawasaki Ernest S Three microarray platforms: an analysis of their concordance in profiling gene expression BMC Genomics |
| title | Three microarray platforms: an analysis of their concordance in profiling gene expression |
| title_full | Three microarray platforms: an analysis of their concordance in profiling gene expression |
| title_fullStr | Three microarray platforms: an analysis of their concordance in profiling gene expression |
| title_full_unstemmed | Three microarray platforms: an analysis of their concordance in profiling gene expression |
| title_short | Three microarray platforms: an analysis of their concordance in profiling gene expression |
| title_sort | three microarray platforms an analysis of their concordance in profiling gene expression |
| url | http://www.biomedcentral.com/1471-2164/6/63 |
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