Table 4.
Genomatix analysis revealed TF binding sites’ loss/gain determined by examined variants. Predictive analysis of proband’s RHO and RLBP1 mutated promoters revealed the possible loss of one group of TF binding sites (NR2F2, RXRA, USF3, MYC, MAX, MLXIPL) for the first gene due to the presence of rs7984, while the substitution of the DEAF1 binding site with the SLC2A4RG one is attributable to rs3743384 for RLBP1. Opt. thresh. = the optimized value defined in a way that a minimum number of matches is found in non-regulatory test sequences (i.e., with this matrix similarity, the number of false positive matches is minimized). Core sim. = the core sequence of a matrix is defined as the (usually four) consecutive highest conserved positions of the matrix. The core similarity is calculated basing on the core sequence. Matrix sim. = the matrix similarity is calculated only if the core similarity reaches a user-defined threshold (core similarity).
| Gene | SNP ID | Lost/ New |
Family/Matrix | TF Name | Family Info | Further Info | Opt. thresh. | Start pos. | End pos. | Strand | Core sim. | Matrix sim. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RHO | rs7984 | lost | V$NR2F/COUPTFII.01 | NR2F2 | Nuclear receptor subfamily 2 factors | Chicken ovalbumin upstream promoter transcription factor 2, NR2F2 homodimer, DR1 sites | 0.8 | 490 | 514 | + | 1 | 0.828 |
| lost | V$RXRF/RXRA.01 | RXRA | RXR heterodimer binding sites | Retinoid X receptor alpha homodimer, DR1 sites | 0.83 | 492 | 516 | + | 1 | 0.894 | ||
| lost | V$EBOX/USF.03 | USF3 | E-box binding factors | Upstream stimulating factor | 0.89 | 494 | 510 | - | 1 | 0.904 | ||
| lost | V$EBOX/MYCMAX.03 | MYC and MAX | E-box binding factors | MYC-MAX binding sites | 0.91 | 495 | 511 | + | 0.842 | 0.919 | ||
| lost | V$CHRE/CHREBP_MLX.01 | MLXIPL | Carbohydrate response elements, consist of two E box motifs separated by 5 bp | Carbohydrate response element binding protein (CHREBP) and Max-like protein X (Mlx) bind as heterodimers to glucose-responsive promoters | 0.82 | 500 | 516 | + | 1 | 0.883 | ||
| RLBP1 | rs3743384 | lost | V$DEAF/NUDR.01 | DEAF1 | Homolog to deformed epidermal autoregulatory factor-1 from D. melanogaster | NUDR (nuclear DEAF-1 related transcriptional regulator protein) | 0.75 | 186 | 204 | - | 1 | 0.801 |
| new | V$HDBP/HDBP1_2.01 | SLC2A4RG | Huntington’s disease gene regulatory region binding proteins | Huntington’s disease gene regulatory region-binding protein 1 and 2 (SLC2A4 regulator and papillomavirus binding factor) | 0.84 | 189 | 207 | - | 1 | 0.863 |