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. 2003 Jul;13(7):1719–1727. doi: 10.1101/gr.533003

Table 2.

GPR Analysis and Validation by the Bootstrap Method

A. (KRNxNOD)F1 transgenic animals compared with healthy nontransgenic littermatesa
Gene GPR score 99.5th %tile p-value Fold change
Cd4 0.841 0.827 0.004 0.12
Il7r 0.773 0.447 <0.004 0.29
Zap70 0.750 0.408 <0.004 0.25
Fcer1g 0.636 0.371 <0.004 2.90
Art2b 0.636 0.363 <0.004 0.36
Cd3e 0.614 0.442 <0.004 0.25
Cd5 0.614 0.409 <0.004 0.25
Bid 0.523 0.385 <0.004 2.46
Ltb 0.523 0.251 <0.004 0.57
Tnfsf6 0.432 0.244 <0.004 0.48
Myd88 0.409 0.341 <0.004 1.98
CD8a 0.386 0.203 <0.004 0.62
B. C57BL/6J malesb
Tnf 0.489 0.135 <0.004 0.33
Csk 0.149 0.246 0.064 1.96
Fcgrt 0.149 0.403 0.100 3.11
Fcer1g 0.128 0.185 0.044 0.82
Tnfrsf1a 0.128 0.093 <0.004 0.63
Tnfrsf1b 0.128 0.101 <0.004 0.86
Ly55d 0.128 0.236 0.084 2.13
Il4ra 0.106 0.136 0.028 0.78
Itgam 0.106 0.110 0.012 0.99
Ltb 0.106 0.226 0.096 1.89
Il10ra 0.085 0.290 0.084 2.06
Ptprc 0.085 0.203 0.096 2.98

The top 12 genes from the GPR output are shown. GPR parameters were Cycle cutoff = 37.5 and threshold p-value = 0.05. The 99.5th percentile score from the bootstrap distribution (250 random resamplings) is shown in the third column. The p-value (fourth column) was compared by dividing the number of scores in the bootstrap probability distribution that were higher than the observed GPR score by the number of random resamplings in the bootstrap analysis (250). The expression fold change (fifth change) was derived after normalization to 18S rRNA. Although GPR ranks genes according to the statistical significance of their change in expression, it does not provide a fold change in gene expression. Thus, following GPR analysis, we computed the fold change normalized to 18S rRNA to gain a sense for the direction and magnitude of change of the highest ranking genes

a

Blood cDNAs from five 8-week-old (KRNxNOD)F1 transgenic animals were compared with five healthy nontransgenic littermates. The IQA gene set was identical to that shown in Table 1, except Fcer1a, Il1r1, Btk, and Scyd1 were replaced by Tbp, Art2b, Hprt, and Gapd, respectively

b

Triplicate blood cDNAs from two 8-week-old C57BL/6J males were compared on the IQA (genes tested as in Table 1)