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: | FC | Uncorr. p† | Corr. p† | FC | p‡ |
| BCL3 (NM_005178) | 1.59 | 2.6×10−5 | 0.03 | 2.15 | 0.005 |
| SOCS3 (NM_003955) | 1.55 | 3.4×10−6 | 0.03 | 1.83 | 0.002 |
| PIM1 (NM_002648) | 1.52 | 6.8×10−6 | 0.03 | 1.67 | 0.001 |
| SBNO2 (NM_014963) | 1.47 | 1.2×10−5 | 0.03 | 1.13 | 0.158 |
| LDHA (NM_005566) | 1.23 | 3.8×10−5 | 0.04 | 1.25 | 0.003 |
| CMAH (NR_002174) | 1.2 | 1.7×10−5 | 0.03 | 1.40 | 0.003 |
| NOG (NM_005450) | −1.32 | 3.1×10−5 | 0.03 | −1.59 | 0.004 |
| PDCD1 (NM_005018) | 1.42 | 1.0×10−5 | 0.03 | ND | ND |
| IGFL2 (NM_001002915) | 1.31 | 1.1×10−7 | 0.002 | ND | ND |
| LOC731186 (XM_001128760) | 1.28 | 2.3×10−5 | 0.03 | ND | ND |
| MUC1 (NM_001044391) | 1.26 | 2.0×10−5 | 0.03 | ND | ND |
| GPRIN3 (CR743148)§ | 1.32 | 2.1×10−4 | 0.049 | ND | ND |
| Additional STAT3-regulated: | |||||
| ID3 (NM_002167) | −1.3 | 5.2×10−4 | 0.16 | ND | ND |
| MYC (NM_002467) | 1.2 | 0.04 | 0.75 | 1.29 | 0.01 |
↵* 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.