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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