Supplementary Table 2. Contribution of low expression genes to the discordance of
differential gene expression list in microarray platforms.
Supplementary Table 2. Inter-site discordance in detection among genes expressed
at low level. For genes expressed at higher than 6,000 molecules/10 ng RNA, there was
>99% correspondence among all 15 microarray sites (5 microarray platforms x 3 sites
each) for detection (using each platform’s call criteria). Here we investigated whether
inter-site discordance in detection may occur among genes expressed at low level and
whether this might contribute to discordance in lists of differentially expressed genes.
Presented for each indicated gene measured to be lowly expressed and to have >2-fold
differential expression between Sample A and B by StaRT-PCR™ (3a) or QuantiGene®
(3b) are the number of microarray sites that detected and showed <2-fold differential
expression, detected the gene and showed >2-fold differential expression, or did not
detect the gene. Each microarray platform defined criteria for presence (detection) call
(MS-3). Specifically, to be present at a site the gene had to be present in >3/5 replicates.
The 22 genes with <1000 transcript molecules/10 ng RNA were included for StaRTPCR™ and the 42 genes with signal less than 2.5 RLU/assay/500 ng RNA were included
for QuantiGene®.
Supplementary Table 2 Summary
1. Among 22 genes expressed less than 1,000 molecules/10 ng RNA and for which
there was >2-fold difference by StaRT-PCR:
a. For those genes with > 2-fold difference by at least one microarray site,
there was 53% inter-site discordance in 2-fold difference detection. This
discordance comprises
i. 19% of the sites detected gene in both samples, but <2-fold
difference.
ii. 34% of the sites did not detect the gene in one or both samples.
b. For those genes with <2-fold difference by each microarray site, 59% of
sites did not detect the gene in one or both samples.
2. For 42 genes expressed less than 2.5 RLU and for which there was >2-fold
difference by StaRT-PCR.
a. For those genes with > 2-fold difference by at least one microarray site,
there was 54% inter-site discordance in 2-fold difference detection. This
discordance comprises:
i. 7% of the sites detected gene in both samples, but <2-fold
difference.
ii. 48% of the sites did not detect the gene in one or both samples.
b. For those genes with <2-fold difference by each microarray site, 89% of
sites did not detect the gene in one or both samples.
Conclusions: Among genes expressed at low level (e.g. <1,000 molecules/10 ng RNA),
for the microarray platforms in this study there was inter-site discordance in lists of genes
measured to have 2-fold or greater A to B difference in expression. This discordance was
associated with inter-site variation in detection of gene in one or both samples or intersite variation in signal-to-analyte response, or both.