Table 1.
Differentially methylated genes between PBC patients (n = 10) and controls (n = 10) in CD4+ T cells, CD8+ T cells, and CD14+ cells from MeDIP array
| Gene symbol | Promoter methylation | Chromosome location | Peak start | Peak end | Molecular function |
|---|---|---|---|---|---|
| CD4+ T cells | |||||
| SHROOM2 | Hypo | Xp22.3 | 9712072 | 9712217 | Protein binding; actin binding; ion channel activity |
| ATP6AP2 | Hypo | Xp11.4 | 40325091 | 40325230 | Receptor activity; protein binding; peptidase activity |
| CXCR3 | Hypo | Xq13 | 70754908 | 70755379 | Protein binding; receptor activity |
| KIAA1210 | Hypo | Xq24 | 118168783 | 118168934 | – |
| RAP2C | Hypo | Xq25 | 131181458 | 131182027 | Nucleotide binding; hydrolase activity |
| HTATSF1 | Hypo | Xq26.3 | 135407214 | 135407962 | RNA binding; nucleotide binding |
| SRPK3 | Hypo | Xq28 | 152699372 | 152700237 | Protein binding; nucleotide binding; protein kinase activity |
| IDH3G | Hypo | Xq28 | 152712248 | 152713105 | Nucleotide binding; catalytic activity; binding |
| SH3KBP1 | Hyper | Xp22.1-p21.3 | 19815048 | 19815499 | Kinase activity; protein binding |
| PHEX | Hyper | Xp22.2-p22.1 | 21960765 | 21961408 | Binding; peptidase activity |
| USP9X | Hyper | Xp11.4 | 40829716 | 40830189 | – |
| EBP | Hyper | Xp11.23-p11.22 | 48265283 | 48265716 | – |
| PQBP1 | Hyper | Xp11.23 | 48638698 | 48639426 | DNA binding; protein binding; transcription regulator activity |
| KDM5C | Hyper | Xp11.22-p11.21 | 53270826 | 53271657 | Catalytic activity; binding; DNA binding; transferase activity |
| IL13RA1 | Hyper | Xq24 | 117745388 | 117746245 | Protein binding; receptor activity |
| UBE2A | Hyper | Xq24 | 118592639 | 118593104 | Catalytic activity; protein binding; nucleotide binding |
| CUL4B | Hyper | Xq23 | 119578240 | 119579025 | Protein binding |
| DCAF12L1 | Hyper | Xq25 | 125513992 | 125514963 | – |
| GPC4 | Hyper | Xq26.1 | 132376771 | 132377010 | Protein binding |
| FAM50A | Hyper | Xq28 | 153325585 | 153326034 | – |
| CD8+ T cells | |||||
| MAGEB2 | Hypo | Xp21.3 | 30142775 | 30143514 | – |
| PIN4 | Hypo | Xq13 | 71318699 | 71318834 | DNA binding; catalytic activity |
| IDH3G | Hypo | Xq28 | 152713172 | 152713419 | Nucleotide binding; catalytic activity; binding |
| GPR143 | Hyper | Xp22.3 | 9693469 | 9693810 | Binding; protein binding |
| CHST7 | Hyper | Xp11.23 | 46317790 | 46318126 | Transferase activity |
| NDUFB11 | Hyper | Xp11.23 | 46889596 | 46889747 | – |
| RBM10 | Hyper | Xp11.23 | 46889596 | 46889747 | RNA binding; nucleotide binding |
| ZXDB | Hyper | Xp11.21 | 57635489 | 57636052 | Nucleic acid binding; binding; protein binding; sequence-specific DNA binding transcription factor activity |
| DOCK11 | Hyper | Xq24 | 117514077 | 117514418 | Enzyme regulator activity; lipid binding; protein binding |
| IL13RA1 | Hyper | Xq24 | 117745582 | 117746125 | Protein binding; receptor activity |
| RNF113A | Hyper | Xq24 | 118889675 | 118890227 | Binding; protein binding |
| AIFM1 | Hyper | Xq26.1 | 129101688 | 129102158 | Catalytic activity; nucleotide binding; protein binding; electron carrier activity; DNA binding |
| MPP1 | Hyper | Xq28 | 153686370 | 153686806 | Kinase activity; protein binding |
| FUNDC2 | Hyper | Xq28 | 153908428 | 153908659 | – |
| RAB39B | Hyper | Xq28 | 154146437 | 154146790 | Nucleotide binding |
| CD14+ cells | |||||
| SYAP1 | Hypo | Xp22.2 | 16647938 | 16648203 | – |
| DYNLT3 | Hypo | Xp21 | 37591227 | 37591696 | – |
| CASK | Hypo | Xp11.4 | 41667126 | 41667877 | Protein binding; ATP binding; protein kinase activity |
| GPR173 | Hypo | Xp11 | 53095323 | 53095568 | G protein-coupled receptor activity |
| CITED1 | Hypo | Xq13.1 | 71441965 | 71442118 | Sequence-specific DNA binding transcription factor activity; protein binding; DNA binding; transcription regulator activity; chromatin binding; hydrolase activity |
| GPRASP1 | Hypo | Xq22.1 | 101790525 | 101790970 | Protein binding |
| RNF128 | Hypo | Xq22.3 | 105824083 | 105824257 | Binding; catalytic activity |
| NSDHL | Hypo | Xq28 | 151750127 | 151750280 | Catalytic activity |
| SSR4 | Hypo | Xq28 | 152710848 | 152711207 | Calcium ion binding |
| KAL1 | Hyper | Xp22.32 | 8659278 | 8659655 | Enzyme regulator activity; protein binding; carbohydrate binding; structural molecule activity |
| SH3KBP1 | Hyper | Xp22.1-p21.3 | 19815148 | 19815397 | Protein binding |
| USP11 | Hyper | Xp11.23 | 46976944 | 46977091 | Peptidase activity; protein binding; hydrolase activity |
| PIM2 | Hyper | Xp11.23 | 48661207 | 48661380 | Protein kinase activity; nucleotide binding |
| PCDH11X | Hyper | Xq21.3 | 90921374 | 90921541 | Calcium ion binding |
| IL1RAPL2 | Hyper | Xq22 | 103696629 | 103696884 | Protein binding; receptor activity |
| PSMD10 | Hyper | Xq22.3 | 107221347 | 107221874 | Protein binding |
| ATG4A | Hyper | Xq22.1-q22.3 | 107221347 | 107221874 | Peptidase activity |
| DCAF12L1 | Hyper | Xq25 | 125513614 | 125513941 | Protein binding |
| FUNDC2 | Hyper | Xq28 | 153908232 | 153908879 | – |