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Table 2 The number of statistically significant differentially expressed genes in naïve and pristane-treated rats according to the individual methods

From: Differential gene expression in pristane-induced arthritis susceptible DA versus resistant E3 rats

Method

Higher in naïve DA rats

Lower in naïve DA rats

Higher in pristane-treated DA rats

Lower in pristane-treated DA rats

Affymetrix (pooled samples)

15 (8800)

24 (8800)

38 (8800)

65 (8800)

Custom-made chips

19 (170)

2 (170)

2 (170)

23 (170)

Real-time PCR

0

0

0 (5)

3 (5)

FACS

4 (7)

3 (7)

3 (7)

2 (7)

ELISA

Total IgE and IgM (3)

0 (3)

Total IgM (3)

Total IgG (3)

  1. To be regarded as differentially expressed with statistical significance, a gene had to fulfil the following threshold values: Affymetrix (pooled samples), differentially expressed with a fold change > 3.0; custom-made oligomer glass chips, differentially expressed with one group t-test P < 0.05; real time PCR, differential expression with Mann–Whitney P < 0.05; FACS, differential geometric mean values with a Mann–Whitney P < 0.05; ELISA, differential plasma concentrations with a Mann–Whitney P < 0.05. The values within parenthesis represent the total number of genes analyzed using the method. ELISA, enzyme linked immunosorbent assay; FACS, fluorescence activated cell sorting.