Table 2.
Top-ranked genes associated with RA (22 autosomes, except chromosome 6)
| Chr. | Gene symbola | No. SNPsb | SCc | No clusteringd | MI clustering | AS clustering | |||
|---|---|---|---|---|---|---|---|---|---|
| p-value | dfe | p-valuef | dfe | p-valuef | dfe | ||||
| 16 | C16orf57 | 2/2 | 1 | 6.06 × 10-8 | 5 | 6.06 × 10-8 (1) | 5 | 1.65 × 10-2 (10) | 3 |
| 21 | KRTAP10-6 | 2/2 | 1 | 8.06 × 10-6 | 6 | 8.06 × 10-6 (2) | 6 | 4.42 × 10-7 (1) | 3 |
| 19 | DEDD2 | 3/3 | 1 | 3.29 × 10-5 | 12 | 3.35 × 10-3 (9) | 2 | 1.84 × 10-6 (2) | 6 |
| 9 | AGPAT2 | 4/4 | 1 | 4.57 × 10-5 | 30 | 4.57 × 10-5 (4) | 5 | 3.30 × 10-3 (9) | 18 |
| 9 | TRAF1 | 3/3 | 1 | 7.35 × 10-5 | 11 | 5.90 × 10-5 (6) | 2 | 8.91 × 10-6 (6) | 6 |
| 15 | ODF3L1 | 4/4 | 1 | 1.00 × 10-4 | 29 | 1.00 × 10-4 (7) | 29 | 1.89 × 10-6 (3) | 17 |
| 19 | RSHL1 | 3/3 | 1 | 1.02 × 10-4 | 12 | 1.53 × 10-3 (8) | 1 | 1.09 × 10-3 (8) | 6 |
| 11 | CDC42BPG | 3/3 | 1 | 1.04 × 10-4 | 12 | 7.95 × 10-1 (10) | 1 | 2.55 × 10-6 (4) | 6 |
| 1 | ADAM15 | 7/7 | 1 | 1.08 × 10-4 | 64 | 5.62 × 10-5 (5) | 49 | 2.05 × 10-5 (7) | 40 |
| 1 | PTPN22 | 6/7 | 0.5 | 1.24 × 10-4 | 34 | 1.52 × 10-5 (3) | 27 | 3.58 × 10-6 (5) | 20 |
aThe genes are sorted by p-value (no clustering). Only the top ten genes in this table were clustered.
bThe number of selected SNPs and the total number of SNPs that were genotyped.
cSC, stability coefficient.
dThe adjusted p-values (no clustering) for all genes in the table are less than 0.001 (1,000 permutations).
edf, degree of freedom, which is the number of clusters subtracted by one.
fThe numbers in parenthesis are the ranks according to MI and AS clustering.
gBold font indicates the genes that have been reported in the literature (PTPN22 and TRAF1) and the genes that we have found that are biologically plausible (ADAM15 and AGPAT2).