Introduction
Methods
Study subjects
CD4+ T-cell RNA processing
Microarray assay
Real-time quantitative polymerase chain reaction
Statistical analysis
Gene Ontology, gene-gene network, and pathway analysis
Results
CD4 T-cell transcriptome in patients with active rheumatoid arthritis versus healthy controls
Gene Ontology analysis of differentially expressed transcripts defined five major gene categories
GO_Id
|
GO_term
|
Count
|
Q
value
|
---|---|---|---|
GO:0006955 | Immune response | 122 | 5.99 × 10−8
|
GO:0002819 | Regulation of adaptive immune response | 23 | 9.37 × 10−4
|
GO:0002678 | Positive regulation of chronic inflammatory response | 12 | 1.38 × 10−3
|
GO:0060333 | Interferon-gamma-mediated signaling pathway | 9 | 6.02 × 10−3
|
GO:0034097 | Response to cytokine stimulus | 17 | 8.61 × 10−3
|
GO:0006915 | Apoptosis | 111 | 1.73 × 10−5
|
GO:0008629 | Induction of apoptosis by intracellular signals | 17 | 4.15 × 10−4
|
GO:0006921 | Cellular component involved in apoptosis | 29 | 2.38 × 10−3
|
GO:0033032 | Regulation of myeloid cell apoptosis | 22 | 7.18 × 10−3
|
GO:0043654 | Recognition of apoptotic cell | 7 | 8.42 × 10−2
|
GO:0050852 | T-cell receptor signaling pathway | 40 | 2.98 × 10−6
|
GO:0007243 | Intracellular protein kinase cascade | 58 | 3.29 × 10−4
|
GO:0016310 | Phosphorylation | 31 | 9.36 × 10−4
|
GO:0016055 | Wnt receptor signaling pathway | 23 | 4.15 × 10−4
|
Corresponding interaction networks among differentially expressed genes in the five major Gene Ontology categories
Corresponding signaling pathways of differentially expressed genes
Path_Id
|
Path_name
|
Path_diffgenes
|
Path_genes
|
Enrichment
|
Q
value
|
---|---|---|---|---|---|
4012 | ErbB signaling pathway | 12 | 87 | 28.122 | 4.88 × 10−14
|
4660 | T-cell receptor signaling pathway | 13 | 108 | 24.542 | 2.69 × 10−14
|
4150 | mTOR signaling pathway | 6 | 52 | 23.525 | 1.71 × 10−7
|
4350 | TGF-β signaling pathway | 10 | 87 | 23.435 | 2.63 × 10−11
|
4210 | Apoptosis | 10 | 89 | 22.909 | 3.01 × 10−11
|
4062 | Chemokine signaling pathway | 18 | 192 | 19.114 | 1.52 × 10−17
|
4010 | MAPK signaling pathway | 23 | 271 | 17.304 | 2.14 × 10−21
|
4630 | Jak-STAT signaling pathway | 12 | 155 | 15.785 | 2.44 × 10−11
|
4310 | Wnt signaling pathway | 11 | 152 | 14.755 | 2.78 × 10−10
|
4620 | Toll-like receptor signaling pathway | 5 | 101 | 10.093 | 9.23 × 10−5
|
4060 | Cytokine-cytokine receptor interaction | 12 | 263 | 9.303 | 6.59 × 10−9
|
5322 | Systemic lupus erythematosus | 5 | 140 | 7.282 | 3.47 × 10−4
|
Probe set ID
|
Gene symbol
|
Fold change
|
Q
value
|
---|---|---|---|
229010_at |
CBL
| 2.22 | 0 |
212435_at |
TRIM33
| 0.61 | 0 |
226294_x_at |
FAM91A1
| 0.33 | 0 |
227817_at |
PRKCB
| 2.26 | 6.101 × 10−16
|
227073_at |
MAP3K2
| 0.50 | 1.296 × 10−14
|
214578_s_at |
ROCK1
| 2.99 | 4.303 × 10−12
|
212073_at |
CSNK2A1
| 0.32 | 5.813 × 10−8
|
1555613_a_at |
ZAP70
| 0.59 | 6.82 × 10−6
|
223300_s_at |
CCDC82
| 0.51 | 6.82 × 10−6
|
212366_at |
ZNF292
| 0.59 | 2.31 × 10−5
|
214917_at |
PRKAA1
| 0.57 | 7.15 × 10−5
|
212249_at |
PIK3R1
| 0.58 | 0.000141 |
231777_at |
CSNK2B
| 3.90 | 0.00076 |
37152_at |
PPARD
| 0.44 | 0.000927 |
231798_at |
NOG
| 1.62 | 0.00133 |
225661_at |
IFNAR1
| 2.16 | 0.002 |
235980_at |
PIK3CA
| 1.70 | 0.00264 |
206359_at |
SOCS3
| 0.62 | 0.00336 |
226660_at |
RPS6KB1
| 0.61 | 0.0101 |
212764_at |
ZEB1
| 1.83 | 0.0125 |
1553725_s_at |
ZNF644
| 0.59 | 0.0187 |
203542_s_at |
KLF9
| 0.61 | 0.0238 |
211930_at |
HNRNPA3
| 0.64 | 0.0344 |