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