Table 2

Fold-change and significance level for genes differentially expressed at inception among peripheral blood CD4 T cells between early arthritis clinic patients with inception diagnoses of RA and non-RA (confirmed at ≥1 year; median 28 months follow-up). The official gene symbol and RefSeq accession number are given as identifiers. Listed STAT3-regulated genes are italicised. 12 genes included in statistically most robust ‘RA signature’ appear in boldface, and additional STAT3-regulated genes referred to in text are also provided

Microarray data (47 RA vs 64 non-RA)qRT-PCR data (32 RA vs 41 non-RA*)
Gene (Accn. No.) 12-Gene RA Signature:FCUncorr. pCorr. pFCp
BCL3 (NM_005178)1.592.6×10−
SOCS3 (NM_003955)1.553.4×10−60.031.830.002
PIM1 (NM_002648)1.526.8×10−60.031.670.001
SBNO2 (NM_014963)1.471.2×10−
LDHA (NM_005566)1.233.8×10−
CMAH (NR_002174)1.21.7×10−50.031.400.003
NOG (NM_005450)−1.323.1×10−50.03−1.590.004
PDCD1 (NM_005018)1.421.0×10−50.03NDND
IGFL2 (NM_001002915)1.311.1×10−70.002NDND
LOC731186 (XM_001128760)1.282.3×10−50.03NDND
MUC1 (NM_001044391)1.262.0×10−50.03NDND
GPRIN3 (CR743148)§1.322.1×10−40.049NDND
Additional STAT3-regulated:
ID3 (NM_002167)−1.35.2×10−40.16NDND
MYC (NM_002467)
  • * Baseline characteristics of Quantitative real-time PCR validation sub-cohort are similar to those of the training cohort overall (table 1) and are given in the online supplementary table S4.

  • Calculations based on normalised expression values of array data; Welch's t-test, raw and multiple-test-corrected p values given (see methods).

  • Calculations based on expression data normalised to the house-keeping gene β-actin (2−ΔCt); Mann–Whitney U test (see methods).

  • § Transcript CR743148 (Illumina Probe ID 6370082) has been retired from NCBI, but the expressed sequence tag corresponds to splice variant(s) within the GPRIN3 gene (chromosome 4.90).

  • FC, linearised fold-change expression in RA relative to non-RA (ie, negative values represent genes downregulated in RA relative to non-RA by n-fold); ND, not done; RA, rheumatoid arthritis.