Table 2.
Differential RNA edited sites in RA, and the differential gene expression of genes harbouring these sites.
| Edited gene | Differentially edited site | Differential gene expression | |||
|---|---|---|---|---|---|
| Chromosome | Edited position | Location of the edited site | logFC | FDR | |
| A. | |||||
| APPL1 | chr3 | 57306834 | UTR3 | 0.7134 | 3.21E-06 |
| ATM | chr11 | 108236469, 108236523 | UTR3 | 1.3121 | 1.75E-14 |
| IFNGR2 | chr21 | 34734080, 34734090 | Intronic | 0.7986 | 6.56E-09 |
| OCIAD1 | chr4 | 48858537 | Intronic | 0.2954 | 0.001720587 |
| RBBP4 | chr1 |
33148623, 33149373
33149376, 33149486, 33149502 |
UTR3 | 0.5668 | 2.82E-08 |
| TM6SF1 | chr15 |
83797712, 83797764
83797765, 83799764 |
Intronic | 0.9344 | 2.67E-06 |
| ZEB1 | chr10 |
31670841, 31670900
31673050, 31673070 |
Intronic | −0.8758 | 1.14E-07 |
| ZNF146 | chr19 | 36724103, 36724207 | Intronic | 0.6606 | 1.77E-07 |
| ANXA4 | chr2 | 70020277 | Intronic | 0.1231 | 0.485437135 |
| PALMD | chr1 | 100148334 | Intronic | −0.0528 | 0.883618553 |
| TMEM51 | chr1 | 15491727, 15491751 | Intronic | 0.427 | 0.088338887 |
| B. | |||||
| ATM | chr11 |
108236469, 108236523
108237815, 108237957 |
UTR3 | 1.2092 | 0.001304199 |
| FPR3 | chr19 | 52319007 | Intronic | 2.0916 | 3.47E-09 |
| GOLGA8 N | chr15 | 32898103, 32898127, 32898133, 32898141, 32898159, 32898163 | UTR3 | −0.6114 | 0.000726014 |
| RBBP4 | chr1 |
33148196, 33148623, 33148691, 33149373, 33149376, 33149486,
33149502 |
UTR3 | 0.4565 | 0.033573174 |
| TIMP3 | chr22 |
33202030, 33202058, 33202064, 33202067, 33203193, 33203215,
33207118 |
Intronic | −0.6604 | 0.024014413 |
| TM6SF1 | chr15 | 83797712, 83797722, 83797764, 83797765, 83799764 | Intronic | 0.9192 | 0.000567265 |
| ZEB1 | chr10 |
31670841, 31670900
31673044, 31673070 |
Intronic | −0.7832 | 0.008743847 |
Abbreviation: RA, rheumatoid arthritis. Tables list genes that are differentially edited along with the location of the edited sites in early RA (A) and in established RA (B) samples, and the differential gene expression analysis of these genes. The genomic coordinates of the edited sites are as per the GRCh37 assembly. A majority of the genes in the vicinity of the identified RNA editing sites are differentially expressed in early RA and established RA and these are highlighted in bold.