Table 1.
RNA-seq analysis of whole blood from SjD cases reveals common and subphenotype-specific differently expressed pcRNAs and lncRNAs
| ENSEMBL ID | Gene symbol | Cytoband | Strand | Chromosome position (hg19) | SjDAll | SjDRo+ | SjDRo− | ||||
| Log2FC | Padj | Log2FC | Padj | Log2FC | Padj | ||||||
| pcRNA | ENSG00000143546 | S100A8 | 1q21.3 | – | chr1:153,362,508–153,363,664 | 1.91 | 3.03E-08 | 2.13 | 1.75E-06 | 1.60 | 6.17E-04 |
| ENSG00000137959 | IFI44L | 1p31.1 | + | chr1:78,619,922–78,646,145 | 1.99 | 3.09E-04 | 2.72 | 4.98E-07 | 0.02 | 9.60E-01 | |
| ENSG00000134321 | RSAD2 | 2p25.2 | + | chr2:6,865,806–6,898,239 | 2.25 | 1.69E-05 | 2.95 | 7.82E-09 | 0.24 | 5.79E-01 | |
| ENSG00000152348 | ATG10 | 5q14.1 | + | chr5:81,972,023–82,276,857 | 1.56 | 1.52E-08 | 1.53 | 9.35E-07 | 1.60 | 4.07E-06 | |
| ENSG00000156467 | UQCRB | 8q22.1 | – | chr8:96,222,947–96,235,546 | 1.52 | 1.35E-13 | 1.54 | 8.08E-08 | 1.51 | 1.14E-06 | |
| ENSG00000165949 | IFI27 | 14q32.12 | + | chr14:94,104,836–94,116,698 | 4.74 | 3.90E-14 | 3.36 | 2.39E-05 | −0.40 | 3.76E-01 | |
| ENSG00000241563 | CORT | 1p36.22 | + | chr1:10,450,031–10,451,998 | −2.59 | 8.40E-03 | −3.22 | 3.95E-03 | −2.07 | 5.69E-02 | |
| ENSG00000229571 | PRAMEF25 | 1p36.21 | + | chr1:13,068,677–13,077,884 | −3.46 | 8.10E-05 | −3.24 | 1.95E-03 | −3.71 | 2.87E-04 | |
| ENSG00000142789 | CELA3A | 1p36.12 | + | chr1:22,001,657–22,012,542 | −2.87 | 5.61E-04 | −2.16 | 1.32E-02 | −1.57 | 7.87E-02 | |
| ENSG00000136834 | OR1J1 | 9q33.2 | – | chr9:122,476,958–122,477,926 | −2.35 | 8.86E-03 | −3.06 | 8.80E-04 | −1.77 | 6.25E-02 | |
| ENSG00000196859 | KRT39 | 17q21.2 | – | chr17:40,958,417–40,966,948 | −2.43 | 1.51E-02 | −1.72 | 9.07E-02 | −4.65 | 1.20E-06 | |
| ENSG00000204978 | ERICH4 | 19q13.2 | + | chr19:41,443,156–41,444,765 | −3.02 | 6.33E-04 | −2.97 | 5.99E-03 | −3.06 | 3.75E-03 | |
| ENSG00000105398 | SULT2A1 | 19q13.33 | – | chr19:47,870,467–47,886,315 | −1.66 | 7.15E-02 | −0.79 | 3.96E-01 | −5.02 | 1.70E-08 | |
| ENSG00000125888 | BANF2 | 20p12.1 | + | chr20:17,693,672–17,735,871 | −2.83 | 1.05E-04 | −2.18 | 7.37E-03 | −4.23 | 5.65E-08 | |
| Antisense lncRNA | ENSG00000237568 | GBP5-AS1 | 1p22.2 | + | chr1:89,260,582–89,269,754 | 1.58 | 3.20E-05 | 1.72 | 2.54E-05 | 1.42 | 1.99E-03 |
| ENSG00000244158 | CALHM6-AS1 | 6q22.1 | – | chr6:116,460,739–116,463,692 | 1.68 | 6.12E-04 | 1.80 | 1.13E-04 | 1.54 | 1.12E-02 | |
| ENSG00000254224 | UQCRB-AS1 | 8q22.1 | + | chr8:96,235,427–96,239,149 | 1.57 | 8.02E-04 | 1.70 | 3.39E-03 | 1.41 | 2.64E-02 | |
| ENSG00000257452 | OAS123-AS1 | 12q24.13 | – | chr12:112,907,628–113,017,751 | 1.24 | 1.83E-02 | 1.83 | 2.61E-04 | 0.00 | 9.98E-01 | |
| ENSG00000259038 | RAD51L1-AS1 | 14q24.1 | – | chr14:68,627,166–68,628,445 | 1.64 | 5.64E-02 | 1.28 | NR | 1.98 | 4.80E-02 | |
| ENSG00000228318 | MX1-AS1 | 21q22.3 | – | chr21:42,813,321–42,814,669 | 1.43 | 4.44E-03 | 2.07 | 4.36E-06 | −0.09 | 8.84E-01 | |
| ENSG00000260990 | TNR-AS1 | 1q25.1 | + | chr1:175,307,218–175,335,459 | −2.52 | 6.47E-03 | −3.16 | 9.46E-04 | −1.99 | 3.62E-02 | |
| ENSG00000261250 | AXDND1-AS1 | 1q25.2 | – | chr1:179,543,201–179,548,922 | −2.43 | 3.35E-03 | −1.91 | 2.86E-02 | −3.68 | 5.32E-05 | |
| ENSG00000224361 | KLHL29-AS1 | 2p24.1 | – | chr2:23,507,043–23,524,344 | −1.68 | 5.51E-02 | −3.09 | 2.49E-03 | −0.82 | 3.93E-01 | |
| ENSG00000225328 | LINC01594 | 2q12.3 | – | chr2:108,167,125–108,217,886 | −2.57 | 4.91E-03 | −1.87 | 4.83E-02 | −4.03 | 2.94E-05 | |
| ENSG00000255420 | CASC23 | 11p15.4 | – | chr11:8,011,278–8,016,520 | −2.53 | 4.46E-03 | −1.96 | 4.61E-02 | −3.59 | 1.97E-04 | |
| ENSG00000276702 | AC010809.3 | 15q14 | – | chr15:33,850,538–33,851,178 | −2.80 | 2.14E-03 | −3.08 | 5.63E-03 | −2.52 | 1.72E-02 | |
| ENSG00000226812 | R3HDML-AS1 | 20q13.12 | – | chr20:44,347,552–44,355,185 | −2.40 | 8.07E-03 | −1.65 | 9.74E-02 | −3.92 | 6.23E-05 | |
| lncRNA | ENSG00000235576 | LINC01871 | 2p25.1 | + | chr2:7,725,801–7,730,705 | 1.16 | 1.78E-05 | 1.01 | 3.26E-03 | 1.33 | 7.67E-05 |
| ENSG00000205837 | LINC00487 | 2p25.2 | – | chr2:6,728,177–6,770,311 | 0.91 | 1.75E-01 | 1.49 | 4.04E-02 | −0.31 | 7.12E-01 | |
| ENSG00000270077 | AP003117.1 | 8p23.1 | + | chr8:97,144,170–97,144,723 | 1.33 | 1.02E-04 | 1.47 | 2.31E-04 | 1.15 | 3.79E-03 | |
| ENSG00000288528 | AP000942.5 | 11q22.2 | – | chr11:102,316,173–102,328,586 | 1.13 | 5.14E-03 | 1.04 | 4.99E-02 | 1.25 | 5.54E-03 | |
| ENSG00000286104 | AC016629.3 | 19q13.43 | + | chr19:58,575,445–58,601,316 | 1.25 | 1.33E-01 | 0.47 | NR | 1.84 | 4.71E-02 | |
| ENSG00000274422 | AC245060.5 | 22q11.22 | – | chr22:22,283,928–22,287,220 | 1.22 | 6.99E-04 | 1.22 | 9.18E-03 | 1.22 | 5.39E-03 | |
| ENSG00000273272 | U62317.3 | 22q13.33 | + | chr22:50,541,108–50,543,011 | 1.03 | 8.18E-05 | 1.44 | 1.67E-07 | 0.36 | 1.83E-01 | |
| ENSG00000285016 | AC017002.3 | 2q13 | – | chr2:111,429,324–111,699,033 | −2.01 | 3.03E-02 | −1.21 | 2.16E-01 | −4.24 | 3.27E-05 | |
| ENSG00000249818 | AC097375.2 | 4q31.3 | – | chr4:151,904,932–151,928,710 | −3.56 | 1.87E-07 | −3.25 | 3.00E-05 | −3.94 | 7.68E-07 | |
| ENSG00000287173 | AL356157.3 | 10q11.21 | + | chr10:44,509,708–44,515,421 | −2.48 | 1.26E-02 | −3.41 | 1.56E-03 | −1.73 | 1.01E-01 | |
| ENSG00000255250 | AP003059.2 | 11q14.2 | + | chr11:86,727,355–86,765,467 | −2.40 | 7.75E-03 | −3.49 | 7.12E-04 | −1.64 | 8.11E-02 | |
| ENSG00000267354 | AC091151.2 | 18q12.3 | + | chr18:45,507,202–45,550,183 | −3.31 | 2.36E-06 | −3.03 | 2.24E-04 | −3.64 | 1.93E-05 | |
| ENSG00000266586 | AC091027.2 | 18q12.3 | – | chr18:78,908,629–78,918,993 | −2.04 | 3.21E-02 | −1.20 | 2.28E-01 | −4.28 | 1.01E-05 | |
| ENSG00000275894 | AL021578.1 | 20q13.12 | – | chr20:45,345,115–45,345,823 | −2.87 | 2.91E-04 | −3.35 | 3.18E-04 | −2.38 | 8.14E-03 | |
| ENSG00000287107 | AL136102.1 | 20q13.13 | + | chr20:48,120,269–48,136,844 | −3.12 | 1.75E-04 | −2.86 | 3.48E-03 | −3.50 | 3.28E-04 | |
| ENSG00000287171 | AC006062.1 | Xq21.1 | + | chrX:8,487,165–8,504,564 | −2.43 | 7.94E-04 | −1.61 | 2.62E-02 | −4.76 | 1.32E-09 | |
Bold indicates top three upregulated and downregulated pcRNAs and lncRNAs in each analysis.
FDR, false discovery rate; lncRNAs, long non-coding RNAs; Log2FC, log2 fold change; Padj, FDR-adjusted p value; pcRNAs, protein-coding RNAs; RNA-seq, RNA sequencing; SjD, Sjögren’s disease; SjDAll, all SjD cases; SjDRo−, anti-Ro negative SjD; SjDRo+, anti-Ro positive SjD.