A set of eight genes were tested using RT-qPCR assays to validate the microarray platform
performance (Table S2). Five were included in the PAM predictive set, SULT1, GST-θ1, AChE,
c20179, and 2_c2341. The remaining three genes were cathepsin L, which was responsive to
PCDD/PCDF, peptidoglycan-recognition protein precursor, which was correlated with PBDE
levels, and C-MYC homolog, regulated by HCB, PBDE and PCB. A Spearman rank-correlation test
was used to assess the correlation between expression values measured with RT-qPCR and
microarrays, respectively, in a total of 64 experiments (see Methods). The Table below indicates
the correlation coefficients calculated for all validated genes. All genes showed high correlation
coefficients (p< 0.05) between microarray and RT-qPCR data either for individual expression
values or group fold-changes. A Mann-Whitney test was also performed on RT-qPCR expression
values of PAM-selected genes to compare MA samples with those collected in AL, CH, and SE,
which showed a significant difference (p<0.01) between the two groups, thus confirming that a
small set of predictive genes allow the discrimination between polluted and unpolluted sites.
Gene
Probe
Spearman’s rho
qPCR/probe
(63 samples)
Spearman’s rho
qPCR/probe
(FC)
PRPP
P_c7409_1
.580(**)
.562(*)
No match
c20179
.634(**)
.568(*)
No match
2c2341
.795(**)
.929(**)
CATL
c2904_AS
.807(**)
.921(**)
GST
c17047
.730(**)
.771(**)
AChE
N_c12315
.662(**)
.809(**)
C-MYC
c3173
.453(**)
.614(*)
SULF
c28883
.722(**)
.794(**)
Correlation between microarray and real-time RT-PCR expression data. Significance of results is
reported at 5% (*) and 1% (**) levels.