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. 2011 Aug;2(8):829–840. doi: 10.1177/1947601911431081

Table 1.

Differential Expression of CRNDE in Colorectal Tissue Samples Assessed by Microarray and qPCR

Microarray
Normal Samples
 Adenoma Samples
 Cancer Samples
Probe set Location Signal averagea Fold changeb P valuec Fold changeb P valuec
Data of others
 238021_s_atd E6 5.2 2.6d 0.022 — —
 238021_s_ate E6 — 14.2 — — —
 238021_s_atf E6 — — — 13.8 <0.001
Discovery data
 238022_at E2, E4, E5 2.8 2.2 0.008 2.6 <0.001
 238021_s_at E6 3.0 4.6 0.001 6.1 <0.001
Validation data
 238022_at E2, E4, E5 2.1 1.3 0.002 1.4 <0.001
 238021_s_at E6 2.1 1.0 0.629 1.1 0.019
Exon array datag
 3692505 Pre-E1A 2.3 0.8 0.354 0.9 0.615
 3692527 E1A 4.8 1.5 0.185 1.5 0.408
 3692526 E1B 5.8 0.8 0.480 1.1 0.880
 3692525 E2 2.2 2.8 0.022 2.6 0.006
 3692524 E4 1.6 8.9 0.012 14.3 0.041
 3692523 In4 3′ 2.0 5.0 0.039 4.3 0.084
 3692522 E5 5′ 1.6 4.5 0.048 4.7 0.083
 3692521 E5 3′ 1.7 14.9 0.005 37.7 0.011
 3692520 In5 2.5 5.8 0.002 8.9 0.017
 3692519 E6 5′ 1.4 1.6 0.031 1.8 0.002
 3692518 E6, mid 1.1 1.2 0.329 1.0 0.754
 3692517 E6 3′ 1.0 1.1 0.181 1.0 0.953
 3692504
 Post-E6
 3.1
 1.4
 0.173
 1.5
 0.334
qPCR
Normal Samples
 Adenoma Samples
 Cancer Samples
CRNDE
 Composition
 ΔCt averagea
 Fold changeb
 P valuec
 Fold changeb
 P valuec
a E1A·E2 6.5 1.8 <0.001 1.4 0.004
b ′E1·E2·E4·′E5·E6 25.9 12.4 <0.001 8.8 <0.001
c ′E1·E2·E3·E4·E5·E6 33.8 >99h 0.002 >99h <0.001
d ′In4E5In5E6 1.6 0.3 0.076 0.3 0.072
e ′In4E5·E6 28.8 7.4 <0.001 5.9 <0.001
f ′E1·E2·E4(In4)E5·E6 24.8 5.6 <0.001 5.0 <0.001
g ′E1B·E2·E4·E5·E6 31.9 15.5 <0.001 12.5 <0.001
h ′E1A·E2·E4·E5·E6 23.3 9.9 <0.001 7.8 <0.001
i ′E1·E2·E4·′E5·E6 30.6 19.8 <0.001 12.5 <0.001
j
 ′In3·E4·E5·E6
 25.9
 9.7
 <0.001
 5.2
 <0.001
qPCR ROC: Adenoma Versus Normal
 qPCR ROC: Cancer Versus Normal
CRNDE
 AUCi
 Thresholdj
 Sensitivity, %
 Specificity, %
 AUCi
 Thresholdj
 Sensitivity, %
 Specificity, %
b 0.939 0.130 91 96 0.921 0.125 85 96
g 0.870 0.180 80 96 0.892 0.095 80 96
h 0.938 0.165 95 96 0.888 0.135 80 96
a

Average for normal samples expressed as the mean probe fluorescence intensity (microarray) or mean value for ΔCt (qPCR), where ΔCt = CtCRNDE – CtHPRT1 and the Ct for each sample is itself a mean value (n = 3).

b

Fold change relative to normal samples. For our microarray data, fold change is given as (2i Neo)mean/(2i Norm)mean, where iNeo and i Norm are the RMA-normalized probe fluorescence intensities for neoplastic and normal samples, respectively. For qPCR data, fold change is given as (2–ΔΔCtNeo)mean/ (2–ΔΔCtNorm)mean, where ΔΔCt = CtCRNDE – CtHPRT1 – CtREF (see above), REF refers to cancer sample TB_163_97 (reference sample), and Neo and Norm relate to neoplastic and normal samples, respectively.

c

By t test using 2i values (as defined above) for microarray, with no need to correct for multiple hypothesis testing, and by Mann-Whitney U test (Gaussian approximation) using 2–ΔΔCt values for qPCR, for which extreme outlier values (5 of 690 values) were not included.

d

Data from GEO Profile GDS2609 for normal-appearing colonic mucosa (sampled >8 cm from tumor) from early-onset nonfamilial CRC patients compared with equivalent tissue from healthy individuals.20 In the absence of any other preadenoma data, we have presented this in the adenoma columns.

e

Data from Sabates-Bellver et al.18

f

Data from Kaneda et al.19

g

Three probe sets located in intron 1 (Fig. 1) have been omitted because their signals showed little or no change in neoplastic tissue (fold change values = 0.97-1.27), and the changes lacked statistical significance (P = 0.24-0.96).

h

The disproportionately large increase is merely a reflection of the fact that this isoform was undetectable in many normal tissue samples, which were therefore assigned a value of Ct = 60 (see Materials and Methods and Suppl. Text S1).

i

AUC = area under receiver operating characteristic (ROC) curve.

j

Fold change (i.e., 2–ΔCt) threshold above which the test outcome was deemed to be positive.