TABLE 1.
Correlation of DNA methylation on differentially expressed genes in transiently infected clones compared to uninfected controls
| Gene group and symbol | Gene name or description | Total no. of meCpGsa | No. of meCpGs (DMR) | meCpG element | Avg TSS distance (bases) | Fold change in expressionb | P valueb |
|---|---|---|---|---|---|---|---|
| Downregulated genes | |||||||
| CYGB | Cytoglobin | 24 | 24 | CGI | 385 | −1.9 | 0.027 |
| IGFBP7 | Insulin-like growth factor binding protein 7 | 7 | 7 | CGI | 278 | −1.9 | 0.001 |
| HTATIP2 | HIV-1 Tat-interactive protein 2, 30 kda | 5 | 5 | CGI | 433 | −5.5 | 0.001 |
| LINC00461 | Long intergenic non-protein coding RNA 461, microRNA 9-2 | 4 | 2 | CGI | 13,050 | −4.9 | 0.005 |
| SETD6 | SET domain containing 6 | 3 | 3 | Shore | 724 | −31.8 | 0.0001 |
| PASD1 | PAS domain containing 1 | 3 | 3 | None | 655 | −7.8 | 0.003 |
| PCDHB6 | Protocadherin beta 6 | 3 | 2 | Shore | 441 | −6.7 | 0.001 |
| HERC5 | Hect domain and RLD 5 | 3 | 3 | CGI | 354 | −2.0 | 0.042 |
| TSTD1 | Thiosulfate sulfurtransferase (rhodanese)-like domain containing 1 | 2 | 2 | CGI | 182 | −50.7 | 0.001 |
| ZC3HAV1L | Zinc finger CCCH-type, antiviral 1-like | 2 | 2 | CGI | 23 | −10.3 | 0.02 |
| TLR2 | Toll-like receptor 2 | 2 | 2 | CGI | 247 | −4.4 | 0.001 |
| NLGN1 | Neuroligin 1 | 2 | 2 | CGI | 713 | −3.2 | 0.022 |
| BEX2 | Brain expressed X-linked 2 | 2 | 2 | CGI | 123 | −3.3 | 0.001 |
| NPR2 | Natriuretic peptide receptor B/guanylate cyclase B (atrionatriuretic peptide receptor B) | 2 | 2 | CGI | 504 | −2.4 | 0.007 |
| RNLS | Renalase, FAD-dependent amine oxidase | 2 | 2 | CGI | 280 | −2.1 | 0.003 |
| SESN3 | Sestrin 3 | 2 | 2 | CGI | 1,269 | −2.1 | 0.001 |
| B3GALNT1 | Beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group) | 2 | 0 | CGI | 389 | −6.3 | 0.001 |
| PCDH10 | Protocadherin 10 | 2 | 0 | CGI | 2,305 | −4.3 | 0.001 |
| SYK | Spleen tyrosine kinase | 2 | 0 | None | 38,241 | −2.3 | 0.001 |
| FAM129B | Family with sequence similarity 129, member B | 2 | 0 | Shore | 61,403 | −1.9 | 0.006 |
| GPR158 | Signal transduction, G-protein-coupled receptor signaling pathway | 1 | 0 | CGI | 1,346 | −22.6 | 0.02 |
| BCAT1 | Branched chain amino acid transaminase 1, cytosolic | 1 | 0 | CGI | 824 | −5.4 | 0.001 |
| CCDC88C | Coiled-coil domain containing 88C | 1 | 0 | CGI | 364 | −2.9 | 0.002 |
| NEFL | Neurofilament, light polypeptide | 1 | 0 | CGI | 63 | −2.8 | 0.003 |
| HRASLS | HRAS-like suppressor | 1 | 0 | CGI | 195 | −2.7 | 0.038 |
| DUOX1 | Dual oxidase 1 | 1 | 0 | CGI | 391 | −2.7 | 0.003 |
| CXCL1 | Chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) | 1 | 0 | Shore | 534 | −2.3 | 0.002 |
| THOC5 | THO complex 5 | 1 | 0 | Shore | 1,042 | −2.1 | 0.013 |
| MEST | Mesoderm-specific transcript homolog (mouse) | 1 | 0 | CGI | 5,220 | −2.0 | 0.033 |
| ERVMER34-1 | Endogenous retrovirus group MER34, member 1 | 1 | 0 | CGI | 408 | −1.9 | 0.009 |
| SLC12A8 | Solute carrier family 12 (potassium/chloride transporters), member 8 | 1 | 0 | Shore | 69,933 | −1.9 | 0.03 |
| ATP5J2-PTCD1 | ATP5J2-PTCD1 readthrough, pentatricopeptide repeat domain 1 | 1 | 0 | None | 8,656 | −1.9 | 0.004 |
| MMRN2 | Multimerin 2 | 1 | 0 | CGI | 14,572 | −1.8 | 0.011 |
| Upregulated genes | |||||||
| FBXL16 | F-box and leucine-rich repeat protein 16 | 20 | 7 | CGI | 9,233 | 3.8 | 0.001 |
| FAM20C | Family with sequence similarity 20, member C | 13 | 5 | Shore | 90,178 | 4.6 | 0.001 |
| COL5A1 | Collagen, type V, alpha 1 | 12 | 3 | None | 83,290 | 2.8 | 0.001 |
| ZIC2 | Zic family member 2 | 8 | 6 | CGI | 682 | 10.7 | 0.013 |
| HS6ST2 | Heparan sulfate 6-O-sulfotransferase 2 | 8 | 7 | CGI | 3,971 | 1.9 | 0.021 |
| TBX3 | T-box 3 | 7 | 5 | CGI | 9,751 | 2.2 | 0.002 |
| EPHB2 | EPH receptor B2 | 7 | 3 | None | 92,791 | 2.0 | 0.011 |
| AUTS2 | Autism susceptibility candidate | 7 | 3 | None | 1,148,930 | 2.9 | 0.001 |
| SOBP | Sine oculis binding protein homolog (Drosophila) | 6 | 6 | CGI | 145,077 | 6.7 | 0.009 |
| AGPAT3 | 1-Acylglycerol-3-phosphate O-acyltransferase 3 | 6 | 4 | None | 65,817 | 2.6 | 0.005 |
| PLXND1 | plexin D1 | 5 | 5 | CGI | 764 | 2.5 | 0.005 |
| APBA2 | Amyloid beta (A4) precursor protein-binding, family A, member 2 | 5 | 3 | CGI | 158,788 | 2.4 | 0.019 |
| LEF1 | Lymphoid enhancer-binding factor 1 | 4 | 2 | CGI | 12,844 | 67.6 | 0.001 |
| KCNH5 | Potassium voltage-gated channel, subfamily H (Eag-related), member 5 | 4 | 2 | CGI | 37,186 | 1.9 | 0.001 |
| LINGO2 | Leucine-rich repeat and Ig domain containing 2 | 3 | 2 | None | 167,376 | 1.95 | 0.033 |
| CYB561 | Cytochrome b-561 | 3 | 0 | CGI | 1,947 | 1.9 | 0.006 |
| WNT5A | Wingless-type MMTV integration site family, member 5A | 2 | 2 | CGI | 6,898 | 46 | 0.001 |
| LINC00478 | Long intergenic non-protein coding RNA 478 | 2 | 2 | None | 315,730 | 1.8 | 0.03 |
| DOHH | Deoxyhypusine hydroxylase/monooxygenase | 2 | 2 | None | 10,309 | 1.81 | 0.011 |
| ADAMTS20 | ADAM metallopeptidase with thrombospondin type 1 motif, 20 | 2 | 0 | CGI | 509 | 4.0 | 0.001 |
| CXADR | Coxsackie virus and adenovirus receptor | 1 | 0 | None | 25,235 | 3.8 | 0.015 |
| SYTL4 | Synaptotagmin-like 4 | 1 | 0 | None | 7,861 | 3.4 | 0.001 |
| HHIP | Hedgehog interacting protein | 1 | 0 | Shore | 985 | 3.4 | |
| RRAGD | Ras-related GTP binding D | 1 | 0 | CGI | 191 | 3.0 | 0.047 |
| METTL20 | Methyltransferase-like 20 | 1 | 0 | None | 1,471 | 2.4 | 0.048 |
| LOC440173 | Uncharacterized LOC440173 | 1 | 0 | CGI | 30,454 | 2.3 | 0.006 |
| LOC283683/LOC646278 | Uncharacterized LOC283683, programmed cell death 6 interacting protein pseudogene | 1 | 0 | None | 52,565 | 2.3 | 0.003 |
| IL21R | Interleukin-21 receptor | 1 | 0 | None | 16,158 | 2.1 | 0.038 |
| TRIML2 | Tripartite motif family-like 2 | 1 | 0 | CGI | 1,280 | 1.9 | 0.04 |
| ABCA1 | ATP-binding cassette, subfamily A (ABC1), member 1 | 1 | 0 | None | 112,091 | 1.9 | 0.003 |
| MYO5B | Myosin VB | 1 | 0 | None | 255,686 | 1.8 | 0.002 |
| CSMD1 | CUB and Sushi multiple domains 1 | 1 | 0 | None | 1,892,786 | 1.8 | 0.041 |
a
meCpG, methylated CpG.
b
Change in expression relative to uninfected controls.