Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR

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Author: Morey, JS
Author: Van Dolah, FM
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Methods Article

Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR

Jeanine S. Morey¹^*, James C. Ryan¹ and Frances M. Van Dolah¹

¹ NOAA Marine Biotoxins Program, Center for Coastal Environmental Health and Biomolecular Research. 219 Fort Johnson Rd., Charleston, SC, 29412. USA.

* To whom correspondence should be addressed: Jeanine S. Morey, NOAA Marine Biotoxins Program, Center for Coastal Environmental Health and Biomolecular Research. 219 Fort Johnson Rd., Charleston, SC, 29412. USA. Email: Jeanine.Morey@noaa.gov

Biol. Proced. Online 2006;8:175-193. doi:10.1251/bpo126
Submitted: May 25, 2006; Accepted: October 29, 2006; Published: December 12, 2006.

Indexing terms: Polymerase Chain Reaction; Microarray Analysis; Gene Expression; Nucleic Acid Amplification Techniques; Reverse Transcriptase Polymerase Chain Reaction; RNA.

Abbreviations: AZA, azaspiracid; Ct, cycle threshold; DA, domoic acid; DR, dose response; IP, intraperitoneally; PbTx, brevetoxin; qPCR, quantitative real-time polymerase chain reaction; RT, reverse transcription; TC, time course.

Figure 1 Enlarged

Fig. 1:

Analysis of data correlation categorized by direction of regulation, spot intensity, and cycle threshold. Correlation of microarray and qPCR data as it relates to (A) direction of regulation, (B) Log (spot intensity), and (C) cycle threshold. Spot intensity data was binned by quartiles and thus, as the intensities from each experiment differed slightly, actual intensities are not indicated in the legend. Asterisks indicate a statistically significant correlation of array and qPCR data (p<0.05). The hatched bars represent the compilation of the five individual data sets, referred to as "all data." Statistical differences of correlations, determined by ANOVA, are indicated by different letters. All correlations were calculated using Spearman’s Rho. The number of samples included in each correlation is shown in the base of the bar. ND, no data (insufficient sample size, n≤2); DA, domoic acid; PbTx, brevetoxin; AZA, azaspiracid; TC, time course; DR, dose response.

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