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Table 2 Gene Set Enrichment Analysis results

From: Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study

Gene set category Drug Direction of regulation Gene set name Sizea NESb NOM p valuec FDR q valued
Reactome gene sets IFX REM > NON-REM
NON-REM > REM Inflammasomes (M1072) 16 1.95 <0.00001 0.07489
TCZ REM > NON-REM
NON-REM > REM
ABT REM> NON-REM
NON-REM > REM Elongation arrest and recovery (M810) 27 1.91 0.00180 0.08880
Regulation of apoptosis (M733) 54 1.96 0.00192 0.09083
Formation of RNA pol II elongation complex (M805) 38 1.85 <0.00001 0.09138
Blood cell gene sets IFX REM > NON-REM
NON-REM > REM
TCZ REM > NON-REM Specific CD19 (Watkins et al., 2009 [15]) 140 −1.70 0.00602 0.02646
B-cell-induced (Allantaz et al., 2012 [16]) 57 −1.56 0.01603 0.08882
NON-REM > REM
ABT REM > NON-REM
NON-REM > REM Specific CD56 (Watkins et al., 2009 [15]) 51 1.60 0.02390 0.02615
NK-cell-induced (Allantaz et al., 2012 [16]) 78 1.63 0.00403 0.02861
  1. Abbreviations:  IFX infliximab, TCZ tocilizumab, ABT abatacept, REM patients with CDAI remission (defined as CDAI ≤2.8) at 6 months of biologic therapy, NON-REM patients without CDAI remission at 6 months of biologic therapy, CDAI clinical disease activity index, NK natural killer, RNA pol II RNA polymerase II
  2. A nominal p value <0.05 and false discovery rate q value <0.1 were considered statistically significant
  3. aNumber of genes found in the gene set from the expression dataset
  4. bNormalized enrichment score is the enrichment score for the gene set after it has been normalized across analyzed gene sets
  5. cNominal p value is the statistical significance of the enrichment score. Nominal p value is not adjusted for gene set size or multiple hypothesis testing
  6. dFalse discovery rate is the estimated probability that the normalized enrichment score represents a false-positive finding