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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.