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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