Table 2.
Fold changes and P-values of top nine upregulated and downregulated genes in Affymetrix microarraya and qRT-PCRb
| Transcript cluster ID | Gene symbol | Description | Microarraya | qRT-PCRb | |||
|---|---|---|---|---|---|---|---|
| Fold-change (linear) | ANOVA P-value | Fold-change (log scale)c | Fold-changed | P-valuee | |||
| Genes upregulated in microarray | |||||||
| TC11002692.hg.1 | MS4A2 | Membrane-spanning 4-domains, subfamily A, member 2 | 1.83 | 0.015 | − 0.03 | 0.978 | 0.824 |
| TC12002538.hg.1 | CHPT1 | Choline phosphotransferase 1 | 1.66 | 0.008 | 1.38 | 2.61 | 7.74E−07 |
| TC0X001829.hg.1 | AMMECR1 | Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1 | 1.51 | 0.043 | − 0.08 | 0.930 | 0.745 |
| TC01002763.hg.1 | WLS | Wntless Wnt ligand secretion mediator | 1.51 | 0.038 | 1.34 | 2.55 | 4.8E−07 |
| TC05000307.hg.1 | NAIP | NLR family, apoptosis inhibitory protein | 1.46 | 0.024 | 0.06 | 1.04 | 0.600 |
| TC11002819.hg.1 | TRIM51EP | Tripartite motif-containing 51E, pseudogene | 1.46 | 0.012 | 0.22 | 1.17 | 0.656 |
| TC01001351.hg.1 | FCER1A | Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide | 1.45 | 0.008 | − 0.13 | 0.91 | 0.297 |
| TC02004639.hg.1 | TNFAIP6 | Tumour necrosis factor, alpha-induced protein 6 | 1.43 | 0.019 | 0.14 | 1.12 | 0.446 |
| TC11003322.hg.1 | CASP5 | Caspase 5 | 1.41 | 0.009 | 0.48 | 1.41 | 2.30E−05 |
| Genes downregulated in microarray | |||||||
|---|---|---|---|---|---|---|---|
| TC05000231.hg.1 | GZMA | Granzyme A | − 1.37 | 0.027 | − 0.38 | 0.770 | 0.0168 |
| TC01003490.hg.1 | XCL2 | Chemokine (C motif) ligand 2 | − 1.37 | 0.0005 | − 0.40 | 0.772 | 0.014 |
| TC04002941.hg.1 | FGFBP2 | Fibroblast growth factor binding protein 2 | − 1.42 | 0.012 | − 0.58 | 0.664 | 0.00162 |
| TC03001304.hg.1 | CX3CR1 | Chemokine (C-X3-C motif) receptor 1 | − 1.42 | 0.002 | − 0.32 | 0.813 | 0.0978 |
| TC01001356.hg.1 | FCRL6 | Fc receptor-like 6 | − 1.48 | 0.01 | − 0.49 | 0.716 | 0.00335 |
| TC19002658.hg.1 | KIR3DL2 | Killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2 | − 1.33 | 0.048 | − 0.45 | 0.745 | 0.0368 |
| TC01003455.hg.1 | SH2D1B | SH2 domain containing 1B | − 1.51 | 0.01 | − 0.31 | 0.810 | 0.0417 |
| TC12001202.hg.1 | KLRB1 | Killer cell lectin-like receptor subfamily B, member 1 | − 1.63 | 0.002 | − 0.21 | 0.871 | 0.588 |
| TC07001296.hg.1 | TARP | TCR gamma alternate reading frame protein | − 1.96 | 0.015 | − 0.30 | 0.816 | 0.0740 |
an = 10 controls, 10 CNP patients. Relative gene expression in microarray was calculated as a ratio of CNP average (log 2) and control average (log 2)
bn = 43 controls and N = 50 CNP participants
cPositive and negative values indicate upregulation and downregulation of genes, respectively, similar to fold-change output in microarray
dValues > 1 and < 1 indicate upregulation and downregulation of the gene, respectively. The relative gene expression in qRT-PCR is expressed as fold-change according to the 2−∆∆Ct method
eP-values were derived using age and gender as control