TABLE 1.
Studies Examining the Correlation Among Microarray Technologies from 2000 to 2003
| Publication | Platforms | Probe ID | Validation | Author'conclusion |
|---|---|---|---|---|
| Kane et al. [2000] | Operson 50mer, PCR probes | Sequence similarity | None | Agreement |
| Huges et al. [2001] | Agilent oligo, cDNA | Sequence similarity; not clearly specified | None | Agreement |
| Yuen et al. [;2002] | Affymetrix, custom cDNA | Sequence similarity (47 genes studied, all sequence confirmed on cDNA platform) | Quantitative (Q) RT-PCR | Agreement |
| Kuo et al. [2002] | Affymetrix, cDNA | Sequence similarity: For each cDNA probe a best matching probe set was identified by sequence alignment. | None | Disagreement |
| Poor correlation between technologies. 56 cell lines from the NCI-60 cell lines studied; independent microarray experiments compared from two labs using different materials and protocols. Cells were cultured independently and all were processed separately. Observed that cross-hybridization of genes to various probes reduced correlation of cDNA arrays to the oligonucleotide arrays. Low abundant transcripts performed poorly. Subsequent re-analysis and improvement by sequence matching [Carter et al., 2005] | ||||
| Kothapalli et al. [2002] | Affymetrix, Incyte cDNA | Sequence similarity: A subset of clones were sequence verified | Northern | Disagreement Noted that a large proportion of cDNAs were incorrectly annotated. Discrepancies were related to probes |
| Li et al. [2002] | Affymetrix, Incyte cDNA | Unigene or Genbank | QR-T-PCR | Disagreement Conclusion based primarily on sensitivity and specificity–Affymetrix found 218 genes differentially expressed versus 4 for cDNA |
| Barezak et al. [2003] | Affymetrix, Operon 70mer | Unigene ID | None | Agreement |
| Carter et al. [2003] | Agilent oligonucleotide, cDNA | Sequence matched | QRT-PCR | Agreement |
| Lee et al. [2003] | Affymetrix, cDNA | UniGene | QRT-PCR | Agreement |
| Wang et al. [2003] | cDNA, Custom oligo | Sequence similarity | RT-PCR | Agreement |
| Rogojina et al. [2003] | Affymetrix, Clontech cDNA | Genbank ID | QRT-PCR and Q-immunoblot | Disagreement Small sample size; examined list of genes that arbitrarily had 1.7-fold or greater change |
| Tan et al. [2003] | Affymetrix, Agilent cDNA, Amersham 30mer | Genbank ID | None | Disagreement Correlations in expression level and significant gene expression were divergent. Subsequent reanalysis and improvement by Shi et al. [2005a] (see Table II) |
| Baum et al. [2003] | Febiot Geniom, Affymetrix, cDNA | Not described | QRT-PCR | Agreement |