Table 3. Top 28 Differentially expressed genes in ACR-Ped70 patients after MTX, Benjamini-Hochberg correction applied.
| P-value | Fold Change | Gene Symbol | Entrez Gene Name | Location | Annotation | |
|---|---|---|---|---|---|---|
| 1 | 0.004 | 12.8 | MALAT1 | metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) | Unknown | Other |
| 2 | 0.004 | 6.7 | CHD9 | chromodomain helicase DNA/binding protein 9 | Cytoplasm | DNA repair |
| 3 | 0.006 | 6 | OSBPL8 | oxysterol binding protein-like 8 | Cytoplasm | Transporter |
| 4 | 0.006 | 3.3 | FBXO42 | F-box protein 42 | Unknown | Ubiquitin cycle |
| 5 | 0.006 | 3.3 | KLF3 | Kruppel-like factor 3 (basic) | Unknown | Transcription Regulator |
| 6 | 0.008 | 3.8 | THAP6 | THAP domain containing 6 | Unknown | Other |
| 7 | 0.008 | 3.5 | ZNF539 | Zinc finger protein 254 | Nucleus | Transcription Regulator |
| 8 | 0.008 | 3.8 | CAP350 | centrosome-associated protein 350 | Cytoplasm | Microtubule Organisation |
| 9 | 0.008 | 5.6 | SYNJ2BP | Synaptojanin 2 binding protein | Cytoplasm | Other |
| 10 | 0.0106 | 3.2 | SPAG9 | sperm associated antigen 9 | Plasma Membrane | Other |
| 11 | 0.0131 | 4.3 | SLC16A7 | solute carrier family 16 (monocarboxylic acid transporters), member 7 | Plasma Membrane | Transporter |
| 12 | 0.0139 | 5.3 | TCF8 (ZEB1) | transcription factor 8 (zinc finger enhancer protein 1) | Nucleus | Transcription Regulator |
| 13 | 0.0216 | 11.5 | C20orf94 | chromosome 20 open reading frame 94 | Unknown | Other |
| 14 | 0.0216 | 3.3 | PTPRC | protein tyrosine phosphatase, receptor type, C | Plasma Membrane | Signal Transduction |
| 15 | 0.0218 | 2.6 | NFATC2IP | nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein | Nucleus | Protein Modification |
| 16 | 0.0218 | 4.7 | ATRX | alpha thalassemia/mental retardation syndrome X-linked | Nucleus | Transcription Regulator |
| 17 | 0.0218 | 4 | ABLIM1 | actin binding LIM protein 1 | Cytoplasm | Cytoskeleton Organization |
| 18 | 0.0218 | 4.6 | EXT1 | Exostoses (multiple) 1 | Unknown | Signal Transduction |
| 19 | 0.0218 | 3.1 | HECTD1 | HECT domain containing 1 | Unknown | Enzyme |
| 20 | 0.0218 | 5.8 | IQGAP1 | IQ motif containing GTPase activating protein 1 | Cytoplasm | Signal Transduction |
| 21 | 0.0218 | 10.8 | OTUD4 | OTU domain containing 4 | Unknown | Other |
| 22 | 0.0222 | -1.8 | EIF4G3 | Eukaryotic translation initiation factor 4 gamma, 3 | Unknown | Protein Biosynthesis |
| 23 | 0.0222 | -1.8 | LOC134492 | NudC domain containing 2 | Unknown | Other |
| 24 | 0.0222 | 2 | SYNCOILIN | Syncoilin, intermediate filament 1 | Unknown | Other |
| 25 | 0.0222 | 2 | ZNF567 | zinc finger protein 567 | Nucleus | Transcription Regulator |
| 26 | 0.0222 | 3.7 | ZNF587 | Zinc finger protein 587 | Unknown | Transcription Regulator |
| 27 | 0.0224 | 4.7 | HNRPD | Heterogeneous nuclear ribonucleoprotein D | Unknown | Other |
| 28 | 0.0237 | 3.8 | BAT1 | HLA-B associated transcript 1 | Nucleus | Enzyme |
Genes in bold are SNP genotyped