Table 3.
Genes upregulated (≥1.5 fold) in lupus patients homozygous for the lupus-associated MECP2 risk haplotype as compared to lupus patients homozygous for the MECP2 protective haplotype
| Gene | Definition/Description | Ratio Risk/Protective | Associative P value |
|---|---|---|---|
| AES | Amino-terminal enhancer of split, transcript variant 3 | 1.55 | 5.63×10−09 |
| AIM2 | Absent in melanoma 2 | 1.62 | 9.06×10−06 |
| ANG | Angiogenin, ribonuclease, RNase A family, 5 | 1.71 | 3.85×10−05 |
| ARSD | Arylsulfatase D, transcript variant 1 | 1.54 | 2.47×10−18 |
| B3GALT4 | UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4 | 1.58 | 1.69×10−21 |
| BTG2 | BTG family, member 2 | 1.77 | 2.07×10−34 |
| BTN3A2 | Butyrophilin, subfamily 3, member A2 | 1.78 | 8.00×10−07 |
| BTN3A3 | Butyrophilin, subfamily 3, member A3, transcript variant 1 | 1.59 | 1.76×10−19 |
| C19ORF10 | Chromosome 19 open reading frame 10 | 1.50 | 1.28×10−13 |
| CCDC53 | Coiled-coil domain containing 53 | 1.77 | 1.31×10−05 |
| CCR6 | Chemokine (C-C motif) receptor 6, transcript variant 2 | 2.53 | 1.76×10−19 |
| CD1C | CD1C antigen, c polypeptide | 1.52 | 1.47×10−08 |
| CD79A | CD79A antigen (immunoglobulin-associated alpha), transcript variant 1 | 2.16 | 4.05×10−20 |
| CD96 | CD96 molecule, transcript variant 1 | 1.89 | 1.69×10−40 |
| CD96 | CD96 molecule, transcript variant 2 | 1.62 | 3.59×10−37 |
| CDKN2C | Cyclin-dependent kinase inhibitor 2C, transcript variant 2 | 1.70 | 7.19×10−05 |
| CEBPD | CCAAT/enhancer binding protein (C/EBP), delta | 1.91 | 6.19×10−38 |
| CECR1 | Cat eye syndrome chromosome region, candidate 1, transcript variant 1 | 3.01 | 1.35×10−33 |
| CHST12 | Carbohydrate (chondroitin 4) sulfotransferase 12 | 1.56 | 4.86×10−05 |
| CLEC2D | C-type lectin domain family 2, member D, transcript variant 3 | 1.86 | 1.38×10−06 |
| CRIM1 | Cysteine rich transmembrane BMP regulator 1 (chordin-like) | 1.51 | 2.74×10−09 |
| CRKRS | Cdc2-related kinase, arginine/serine-rich | 2.23 | 7.28×10−10 |
| DHRS8 | Hydroxysteroid (17-beta) dehydrogenase 11 | 1.58 | 3.14×10−28 |
| EAF2 | ELL associated factor 2 | 1.70 | 2.97×10−07 |
| EDG6 | Endothelial differentiation, G-protein-coupled receptor 6 | 2.04 | 5.91×10−09 |
| EVI2B | Ecotropic viral integration site 2B | 1.75 | 6.98×10−18 |
| FAM46C | Family with sequence similarity 46, member C | 2.92 | 9.17×10−20 |
| FAM55C | Family with sequence similarity 55, member C | 1.62 | 1.42×10−08 |
| FLJ11000 | Hypothetical protein FLJ11000 | 2.26 | 4.20×10−28 |
| FLJ20021 | PREDICTED: Hypothetical LOC90024 | 1.52 | 8.68×10−09 |
| FLJ43692 | ARHGEF5-like | 1.83 | 4.81×10−05 |
| G1P3 | Interferon, alpha-inducible protein (clone IFI-6-16), transcript variant 1 | 1.53 | 3.20×10−05 |
| GPR18 | G protein-coupled receptor 18 | 2.02 | 1.92×10−10 |
| GSDML | Gasdermin-like | 1.76 | 6.37×10−114 |
| H2AFJ | H2A histone family, member J, transcript variant 2 | 1.66 | 2.26×10−04 |
| HCST | Hematopoietic cell signal transducer, transcript variant 1 | 1.64 | 4.50×10−04 |
| HIST1H1C | Histone cluster 1, H1c | 2.03 | 2.82×10−07 |
| HIST1H2BH | Histone cluster 1, H2bh | 1.52 | 1.41×10−12 |
| HIST1H4K | Histone cluster 1, H4k | 1.69 | 2.71×10−06 |
| HLA-E | Histocompatibility complex, class I, E | 1.77 | 1.01×10−17 |
| HLA-F | Major histocompatibility complex, class I, F | 1.75 | 2.64×10−45 |
| HLA-H | Major histocompatibility complex, class I, H | 2.33 | 1.21×10−09 |
| HS.276808 | CDNA FLJ43371 fis, clone NTONG2005969 | 1.63 | 1.30×10−06 |
| HS.487766 | CDNA clone L17N670205n1-10-D09 5 | 1.78 | 3.46×10−09 |
| IFI35 | Interferon-induced protein 35 (IFI35), mRNA. | 1.53 | 1.73×10−04 |
| IFI6 | Interferon, alpha-inducible protein 6 (IFI6), transcript variant 2 | 2.13 | 4.86×10−05 |
| IFITM1 | Interferon induced transmembrane protein 1 | 2.03 | 1.03×10−05 |
| IFITM3 | Interferon induced transmembrane protein 3 | 3.41 | 0.00 |
| IGJ | Immunoglobulin J polypeptide | 2.89 | 8.82×10−21 |
| IRF7 | Interferon regulatory factor 7, transcript variant b | 1.87 | 2.13×10−14 |
| IRF7 | Interferon regulatory factor 7, transcript variant c | 1.77 | 2.86×10−18 |
| ISG20 | Interferon stimulated exonuclease gene 20kDa | 2.00 | 5.27×10−08 |
| ITGAL | Integrin, Lymphocyte function-associated antigen 1; alpha polypeptide | 1.87 | 2.43×10−15 |
| ITM2B | Integral membrane protein 2B | 3.15 | 2.78×10−46 |
| ITM2C | Integral membrane protein 2C, transcript variant 2 | 1.66 | 2.92×10−04 |
| ITM2C | Integral membrane protein 2C, transcript variant 1 | 1.58 | 1.09×10−03 |
| KIAA0125 | KIAA0125 | 2.47 | 6.86×10−16 |
| LBA1 | PREDICTED: Lupus brain antigen 1 | 1.72 | 1.59×10−08 |
| LDLR | Low density lipoprotein receptor (familial hypercholesterolemia) | 1.71 | 2.35×10−10 |
| LIME1 | Lck interacting transmembrane adaptor 1 | 1.76 | 2.69×10−21 |
| LMBRD1 | LMBR1 domain containing 1 | 1.57 | 1.62×10−05 |
| LMO4 | LIM domain only 4 | 1.80 | 1.67×10−05 |
| LOC387882 | Hypothetical protein | 1.60 | 4.73×10−08 |
| LOC541471 | PREDICTED: Hypothetical LOC541471 | 1.71 | 3.16×10−17 |
| LOC554223 | PREDICTED: Hypothetical LOC554223, transcript variant 3 | 1.57 | 3.18×10−24 |
| LY6E | Lymphocyte antigen 6 complex, locus E | 1.82 | 1.44×10−04 |
| MGC13057 | Hypothetical protein MGC13057 | 2.56 | 3.06×10−07 |
| MGC24039 | Hypothetical protein MGC24039 | 1.68 | 4.01×10−13 |
| MGC29506 | Hypothetical protein MGC29506 | 1.74 | 1.33×10−15 |
| MGST3 | Microsomal glutathione S-transferase 3 | 1.60 | 4.75×10−06 |
| MID1IP1 | MID1 interacting protein 1 (gastrulation specific G12-like (zebrafish)) | 1.50 | 3.35×10−07 |
| NCF4 | Neutrophil cytosolic factor 4, 40kDa, transcript variant 1 | 1.85 | 6.11×10−61 |
| NPC2 | Niemann-Pick disease, type C2 | 1.54 | 6.04×10−07 |
| P2RY5 | Purinergic receptor P2Y, G-protein coupled, 5 | 2.59 | 5.91×10−07 |
| PHGDH | Phosphoglycerate dehydrogenase | 1.54 | 6.46×10−06 |
| PIM2 | Pim-2 oncogene | 1.61 | 4.07×10−17 |
| PIP3-E | Phosphoinositide-binding protein PIP3-E | 2.30 | 4.37×10−06 |
| PNOC | Prepronociceptin | 1.75 | 7.40×10−16 |
| PRDM1 | PR domain containing 1, with ZNF domain, transcript variant 1 | 1.67 | 1.42×10−06 |
| PRDX4 | Peroxiredoxin 4 | 1.52 | 1.01×10−12 |
| PTPRCAP | Protein tyrosine phosphatase, receptor type, C-associated protein | 1.68 | 1.55×10−07 |
| PYCARD | PYD and CARD domain containing, transcript variant 3 | 1.54 | 4.76×10−04 |
| RABAC1 | Rab acceptor 1 (prenylated) | 1.54 | 1.09×10−09 |
| RNASET2 | Ribonuclease T2 | 1.94 | 2.42×10−06 |
| RNF36 | Ring finger protein 36, transcript variant b | 2.00 | 8.84×10−12 |
| RNF36 | Ring finger protein 36, transcript variant a | 1.72 | 2.74×10−10 |
| S100A10 | S100 calcium binding protein A10 | 2.42 | 1.76×10−15 |
| SCOTIN | Scotin | 1.61 | 3.53×10−13 |
| SGK | Serum/glucocorticoid regulated kinase | 2.08 | 3.28×10−04 |
| SLC27A3 | Solute carrier family 27 (fatty acid transporter), member 3 | 1.62 | 9.09×10−09 |
| SORT1 | Sortilin 1 | 1.62 | 1.81×10−10 |
| SPRY2 | Sprouty homolog 2 (Drosophila) | 1.63 | 3.95×10−07 |
| SSR4 | Signal sequence receptor, delta (translocon-associated protein delta) | 1.67 | 3.93×10−10 |
| ST3GAL1 | ST3 beta-galactoside alpha-2,3-sialyltransferase 1, transcript variant 2 | 1.85 | 4.02×10−36 |
| TBX15 | T-box 15 | 1.66 | 1.33×10−12 |
| TCL6 | T-cell leukemia/lymphoma 6, transcript variant TCL6d1 | 1.54 | 2.56×10−29 |
| TMEM156 | Transmembrane protein 156 | 1.50 | 3.11×10−07 |
| TNFRSF17 | Tumor necrosis factor receptor superfamily, member 17 | 1.50 | 8.82×10−08 |
| TNFRSF7 | Tumor necrosis factor receptor superfamily, member 7 | 2.43 | 2.91×10−07 |
| TRIB1 | Tribbles homolog 1 (Drosophila) | 1.57 | 5.01×10−05 |
| TRIM69 | Tripartite motif-containing 69, transcript variant b | 1.90 | 5.28×10−11 |
| TXNDC11 | Thioredoxin domain containing 11 | 1.66 | 1.90×10−05 |
| TXNDC5 | Thioredoxin domain containing 5, transcript variant 1 | 1.82 | 4.20×10−08 |
| VIM | Vimentin | 2.03 | 3.97×10−06 |
| XBP1 | X-box binding protein 1, transcript variant 1 | 1.90 | 2.44×10−10 |
| XBP1 | X-box binding protein 1, transcript variant 2 | 1.87 | 2.73×10−08 |
| ZBP1 | Z-DNA binding protein 1 | 2.09 | 1.96×10−25 |
| ZFP36 | Zinc finger protein 36, C3H type, homolog (mouse) | 1.77 | 1.04×10−31 |
| ZSWIM6 | PREDICTED: Zinc finger, SWIM-type containing 6 | 1.52 | 2.05×10−05 |