Table 1 Genes that were differentially expressed between probands (n = 20) with systemic autoimmune disease and unrelated, matched controls (n = 40)
Accession | Annotation | Fold changea | Pvalueb | FDR | Function/Category |
|---|---|---|---|---|---|
Increased expression in probands | Â | Â | Â | Â | Â |
TNFAIP6 | Tumor necrosis factor-alpha-induced protein 6 | 2.2 | 1.5 × 10-5 | 0.051 | Co-factor, immune |
HP | Haptoglobin | 2.2 | 2.0 × 10-5 | 0.051 | Carrier, transport |
HPR | Haptoglobin-related protein | 2.3 | 3.5 × 10-5 | 0.059 | Carrier, transport |
ANXA3 | Annexin A3 | 2.8 | 5.1 × 10-5 | 0.074 | Regulation, signaling |
APOBEC3A | Apolipoprotein B mRNA editing enzyme 3A | 1.4 | 5.8 × 10-5 | 0.074 | Regulation, translation |
EIF2AK2 | Eukaryotic translation initiation factor 2-alpha kinase 2 | 2.4 | 7.1 × 10-5 | 0.074 | Regulation, translation |
BMX | Non-receptor tyrosine kinase | 2.2 | 8.6 × 10-5 | 0.074 | Kinase, signaling |
CEACAM6 | Carcinoembryonic Ag-related cell adhesion molecule 6 | 4.7 | 8.7 × 10-5 | 0.074 | Receptor, targeting |
PLSCR1 | Phospholipid scramblase 1 | 2.3 | 1.0 × 10-4 | 0.074 | Regulation, immune |
LTF | Lactotransferrin | 2.3 | 1.1 × 10-4 | 0.074 | Regulation, immune |
TNFSF10 | Tumor necrosis factor ligand 10 | 1.6 | 1.4 × 10-4 | 0.074 | Cytokine, immune |
OASL | 2'-5'-Oligoadenylate synthetase-like | 2.2 | 1.7 × 10-4 | 0.074 | Binding, thyroid receptor |
MAP2K6 | Mitogen-activated protein kinase kinase 6 | 1.4 | 2.2 × 10-4 | 0.080 | Kinase, signaling |
ZCCHC2 | Zinc finger protein | 1.5 | 2.4 × 10-4 | 0.082 | Unknown, signaling |
INHBB | Inhibin, beta B | 2.3 | 2.7 × 10-4 | 0.085 | Ligand, signaling |
DEFA4 | Defensin, alpha 4, corticostatin | 2.3 | 2.9 × 10-4 | 0.088 | Ligand, signaling |
IFI27 | Interferon, alpha-inducible protein 27 | 7.2 | 3.0 × 10-4 | 0.088 | Unknown, immune |
SLC22A4 | Solute carrier family 22, member 4 | 1.7 | 3.3 × 10-4 | 0.088 | Transport |
IL1RN | Interleukin 1 receptor antagonist | 1.7 | 3.4 × 10-4 | 0.088 | Ligand, immune |
RRAGD | Ras-related GTP-binding protein D | 1.3 | 3.4 × 10-4 | 0.088 | Ligand, signaling |
DEGS1 | Degenerative spermatocyte homolog 1 | 1.1 | 3.9 × 10-4 | 0.093 | Enzyme, metabolism |
PGAP1 | GPI deacylase | 1.3 | 3.9 × 10-4 | 0.093 | Enzyme, signaling |
F5 | Coagulation factor V | 1.4 | 4.2 × 10-4 | 0.094 | Ligand, coagulation |
CDS2 | CDP-diacylglycerol synthase | 1.2 | 4.6 × 10-4 | 0.097 | Enzyme, metabolism |
HIST1H2AB | Histone 1, H2ab | 1.3 | 4.7 × 10-4 | 0.097 | Chromatin, structural |
Decreased expression in probands | Â | Â | Â | Â | Â |
PACSIN1 | Protein kinase C substrate 1 in neurons | -1.4 | 3.3 × 10-6 | 0.042 | Kinase, signaling |
KRTCAP2 | Keratinocyte-associated protein 2 | -1.2 | 5.9 × 10-6 | 0.042 | Enzyme, structural |
FCER1A | Fc fragment of high affinity IgE receptor | -1.9 | 9.2 × 10-6 | 0.042 | Receptor, immune |
FYN | Oncogene | -1.3 | 9.8 × 10-6 | 0.042 | Kinase, signaling |
SYTL2 | Synaptotagmin-like 2 | -1.5 | 1.0 × 10-5 | 0.042 | Unknown, immune |
CD99 | MIC2, single-chain type-1 glycoprotein | -1.2 | 1.8 × 10-5 | 0.051 | Receptor, immune |
PECI | Peroxisomal D3,D2-enoyl-CoA isomerase | -1.3 | 3.3 × 10-5 | 0.059 | Enzyme, metabolism |
CD81 | Target of antiproliferative antibody 1 | -1.2 | 3.4 × 10-5 | 0.059 | Receptor, immune |
PBX4 | Pre-B-cell leukemia transcription factor 4 | -1.4 | 7.7 × 10-5 | 0.074 | Regulation, transcription |
DYRK2 | Tyrosine-phosphorylation regulated kinase 2 | -1.2 | 8.1 × 10-5 | 0.074 | Kinase, signaling |
ZBTB5 | Zinc finger and BTB domain containing 5 | -1.2 | 9.4 × 10-5 | 0.074 | Regulation, transcription |
PABPC3 | Poly(A)-binding protein 3 | -1.3 | 9.8 × 10-5 | 0.074 | Regulation, translation |
NELL2 | NEL-like 2 | -1.3 | 1.0 × 10-4 | 0.074 | Mitogen, cell division |
LOC100133315 | Unknown cation channel/receptor | -1.2 | 1.0 × 10-4 | 0.074 | Receptor, signaling |
DNAJA3 | DnaJ (Hsp40) homolog A3 | -1.3 | 1.2 × 10-4 | 0.074 | Chaperone, transport |
EIF3S6IP | Eukaryotic translation initiation factor 3, subunit 6 | -1.3 | 1.2 × 10-4 | 0.074 | Regulation, translation |
EIF3S8 | Eukaryotic translation initiation factor 3, subunit 8 | -1.2 | 1.2 × 10-4 | 0.074 | Regulation, translation |
RBMX | RNA-binding motif protein | -1.1 | 1.2 × 10-4 | 0.074 | Regulation, transcription |
GZMK | Granzyme K | -1.4 | 1.3 × 10-4 | 0.074 | Enzyme, immune |
DNMT1 | DNA (cytosine 5)-methyltransferase 1 | -1.3 | 1.3 × 10-4 | 0.074 | Enzyme, metabolism |
ZNF219 | Zinc finger protein 219 | -1.2 | 1.3 × 10-4 | 0.074 | Regulation, transcription |
DVL1 | Dishevelled homologue (Drosophila) | -1.2 | 1.4 × 10-4 | 0.074 | Mitosis, signaling |
IMP3 | U3 small ribonucleoprotein homologue (yeast) | -1.2 | 1.5 × 10-4 | 0.074 | Structural, translation |
ANAPC5 | Anaphase promoting complex subunit 5 | -1.2 | 1.5 × 10-4 | 0.074 | Enzyme, cell cycle |
AOF2 | Amine oxidase (flavin containing) domain 2 | -1.2 | 1.6 × 10-4 | 0.074 | Regulation, transcription |
GPRASP1 | G protein-coupled receptor | -1.4 | 1.6 × 10-4 | 0.074 | Receptor, signaling |
LTK | Leukocyte tyrosine kinase | -1.3 | 1.6 × 10-4 | 0.074 | Kinase, immune |
MTA1 | Metastasis-associated 1 | -1.2 | 1.6 × 10-4 | 0.074 | Regulation, transcription |
UXT | Ubiquitously expressed transcript | -1.2 | 1.6 × 10-4 | 0.074 | Regulation, transcription |
KLRB1 | Killer cell lectin-like receptor B1 | -1.6 | 1.7 × 10-4 | 0.074 | Receptor, immune |
SEMA4C | Semaphorin 4C | -1.3 | 1.7 × 10-4 | 0.074 | Neural development |
STMN3 | Stathmin-like 3 | -1.4 | 2.0 × 10-4 | 0.079 | Cytoskeletal, signaling |
ATP1A1 | ATPase Na+/K+ transporter | -1.2 | 2.0 × 10-4 | 0.079 | Transporter, signaling |
PSBP | Prostatic steroid-binding protein | -1.3 | 2.2 × 10-4 | 0.080 | Receptor, signaling |
RPL18 | Ribosomal protein L18 | -1.3 | 2.2 × 10-4 | 0.080 | Structural, translation |
RNF220 | Ring finger protein | -1.1 | 2.2 × 10-4 | 0.080 | Unknown |
SPOCK2 | Sparc/osteonectin/proteoglycan (testican) 2 | -1.2 | 2.3 × 10-4 | 0.081 | Extracellular, structural |
DDX28 | DEAD box polypeptide | -1.2 | 2.3 × 10-4 | 0.081 | RNA helicase, transcription |
SRP46 | Splicing factor, arginine/serine-rich, 46 kDa | -1.3 | 2.4 × 10-4 | 0.082 | Regulation, transcription |
EIF3S7 | Eukaryotic translation initiation factor 3S7 | -1.2 | 2.5 × 10-4 | 0.084 | Regulation, translation |
TNFRSF25 | Tumor necrosis factor receptor 25 | -1.3 | 2.6 × 10-4 | 0.085 | Receptor, immune |
MYBL1 | v-Myb myeloblastosis viral oncogene homolog | -1.4 | 2.7 × 10-4 | 0.085 | Regulation, transcription |
UBE2I | Ubiquitin-conjugating enzyme E2I | -1.1 | 2.8 × 10-4 | 0.087 | Enzyme, regulation |
PABPC1 | Poly(A)-binding protein | -1.3 | 3.0 × 10-4 | 0.088 | Regulation, translation |
LDOC1L | Leucine zipper, downregulated in cancer 1-like | -1.4 | 3.1 × 10-4 | 0.088 | Unknown |
LGR6 | Leucine-rich repeat-containing G protein receptor 6 | -1.6 | 3.1 × 10-4 | 0.088 | Receptor, signaling |
AES | Amino-terminal enhancer of split | -1.1 | 3.2 × 10-4 | 0.088 | Regulation, transcription |
CXCR3 | Chemokine receptor 3 | -1.3 | 3.2 × 10-4 | 0.088 | Receptor, immune |
ATP5G2 | ATP synthase, mitochondrial F0 complex | -1.2 | 3.3 × 10-4 | 0.088 | Enzyme, metabolism |
RPLP2 | Ribosomal protein P2 | -1.3 | 3.3 × 10-4 | 0.088 | Structural, translation |
TC2N | Membrane targeting C2 domain | -1.4 | 3.6 × 10-4 | 0.090 | Unknown, signaling |
ERGIC3 | Breast cancer antigen 84 | -1.2 | 3.8 × 10-4 | 0.092 | Unknown, cell growth |
GPR183 | Epstein-Barr virus induced gene 2 | -1.5 | 3.9 × 10-4 | 0.093 | Receptor, signaling |
CSNK1E | Casein kinase 1, epsilon | -1.2 | 4.1 × 10-4 | 0.094 | Kinase, regulation |
CRIP1 | Cysteine-rich protein 1 | -1.3 | 4.1 × 10-4 | 0.094 | Zn-binding, transport |
ARIH2 | Ariadne homolog 2 | -1.1 | 4.2 × 10-4 | 0.094 | Ubiquitin ligase, regulation |
POLS | DNA polymerase sigma | -1.2 | 4.2 × 10-4 | 0.094 | Enzyme, metabolism |
PUF60 | Ro-RNP-binding protein | -1.2 | 4.3 × 10-4 | 0.096 | RNP-binding, regulation |
MFNG | Fucose-specific β-1,3-N-acetylglucosaminyltransferase | -1.2 | 4.7 × 10-4 | 0.097 | Enzyme, development |
PRPSAP2 | Phosphoribosyl pyrophosphate synthetase protein 2 | -1.2 | 4.7 × 10-4 | 0.097 | Enzyme, metabolism |
STAG3 | Stromal antigen 3 | -1.3 | 4.7 × 10-4 | 0.097 | Cohesion subunit, meiosis |
FBL | Fibrillarin | -1.2 | 4.9 × 10-4 | 0.098 | snRNP-binding, pre-rRNA |
RPS19 | Ribosomal protein S19 | -1.3 | 4.9 × 10-4 | 0.098 | Structural, translation |
DDB1 | Damage-specific DNA-binding protein 1 | -1.2 | 5.0 × 10-4 | 0.098 | DNA repair |
FBXO21 | F-box protein 21 | -1.2 | 5.0 × 10-4 | 0.098 | Ubiquitin ligase, regulation |
PTDSS1 | Phosphatidylserine synthase 1 | -1.2 | 5.1 × 10-4 | 0.100 | Enzyme, metabolism |
AKR1B1 | Aldo-keto reductase family 1, member B1 | -1.2 | 5.2 × 10-4 | 0.100 | Enzyme, metabolism |