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Table 2 List of genes differentially expressed between anti-TNF responders and non-responders

From: Lower peripheral helper T cell levels in the synovium are associated with a better response to anti-TNF therapy in rheumatoid arthritis

Gene symbol Accession Definition Fold change P value
Genes significantly overexpressed in non-responders, week 0
PIK3CD* NM_005026.2 Phosphoinositide-3-kinase, catalytic, − 1.56 7.11e−18
delta polypeptide   
REEP4 NM_025232.2 Receptor accessory protein 4 − 1.50 7.14e−17
HCLS1 NM_005335.3 Hematopoietic cell-specific Lyn substrate 1 − 1.63 4.38e−09
GCDH NM_013976.2 Glutaryl-coenzyme A dehydrogenase − 1.50 3.2e−07
ADA NM_000022.2 Adenosine deaminase − 1.73 7.15e−07
NT5DC2 NM_022908.1 5′-Nucleotidase domain containing 2 − 1.86 7.7e−07
SERPINH1 NM_001235.2 Serpin peptidase inhibitor, clade H, member 1 − 1.66 1.67e−06
Genes significantly overexpressed in responders, week 0
CX3CL1* NM_002996.3 Chemokine (C-X3-C motif) ligand 1 1.94 7.4e−12
PLS3 NM_005032.3 Plastin 3 (T isoform) 1.71 1.97e−10
DIXDC1 NM_033425.1 DIX domain containing 1 1.90 9.29e−10
TMOD1 NM_003275.1 Tropomodulin 1 2.10 1.56e−08
PCOLCE2 NM_013363.2 Procollagen C-endopeptidase enhancer 2 2.45 3.34e−07
PPP1R3C  NM_005398.3 Protein phosphatase 1, regulatory (inhibitor) 2.13 3.64e−07
Subunit 3C   
CRTAP NM_006371.3 Cartilage associated protein 1.58 4.78e−07
PRELP NM_002725.3 Proline/arginine-rich end leucine-rich repeat 2.02 6.42e−07
Protein, transcript variant 1   
DKFZP686A01247 NM_014988.1 Hypothetical protein 2.30 7.13e−07
UNQ689 NM_212557.1 RSTI689 5.09 9.54e−07
OR2A9P NR_002157.1 Olfactory receptor, family 2, subfamily A, 2.01 1.94e−06
member 9   
Genes significantly overexpressed in non-responders, week 20
RPS6KA2 NM_001006932.1 Ribosomal protein S6 kinase, 90 kDa − 1.53 3.10e−07
Polypeptide 2   
LIPA NM_000235.2 Lipase A, lysosomal acid, cholesterol esterase − 1.50 1.50e−07
(Wolman disease)   
ALPL NM_000478.2 Alkaline phosphatase, liver/bone/kidney − 2.77 7.90e−07
Genes significantly overexpressed in responders, week 20
PDE4B NM_002600.2 Phosphodiesterase 4B, cAMP-specific 1.57 1.10e−07
  1. The list of genes that are significant after Bonferroni correction and that show an > 1.5 absolute fold change between the two groups are shown. Fold change is calculated contrasting the mean expression in the anti-TNF responder group to the mean expression in the non-responder. *Top differentially expressed genes validated using RT-QPCR