Table 5.
Prediction of TFBS by the software FIMO for rs368234815, rs12980275, rs12979860, rs8099917, and rs4803217
| SNP/allele | Transcription factor | Modification (in the presence of the minor allele) | Strand | p-value/q-value† | Matched sequence |
|---|---|---|---|---|---|
| rs368234815/∆G | PLAG1 like zinc finger 1 | Removed | “+” | 7.49e-05/0.0636 | CGGGGGGCCT |
| rs12979860/ T | Transcription factor E2F7 | Removed | “+” | 2.49e-05/0.0288 | GAAGGCGCGAACC |
| rs12979860/ T | Oxysterols receptor LXR-alpha: Retinoid X receptor alpha (Nr1h3::Rxra) | Added | “+” | 6.03e-05/0.0423 | TGAACCAGGGTTGAATTGC |
| rs12979860/ T | Oestrogen Related Receptor Alpha (ESRRA) | Removed | – | 4.71e-05/0.0498 | TCAGGGTCAAT |
| rs12979860/ T | MAX Dimerization Protein (MGA) | Added | “+” | 9.32e-05/0.00347 | AGGCGTGA |
| rs12979860/ T | T-box brain protein 1 (TBR1) | Added | “+” | 5.29e-05/0.0495 | AGGCGTGAAC |
| rs4803217/ A | Transcription factor HES-2 | Added | “+” | 7.76e-05/0.00974 | TTAAGACAAGTGG |
| rs4803217/ A | DNA (cytosine-5)-methyltransferase 1 (DNMT1) | Removed | “+” | 9.7e-06/0.0499 | CCCCGCTGGC |
| rs4803217/ A | Homeobox protein NKX3–2 | Removed | “+” | 7.51e-05/0.0107 | AGCCAAGTGGC |
| rs4803217/ A | POU domain, class 6, transcription factor 1 (POU6F1) | Removed | “+” | 4.41e-05/0.0279 | AATAAATTAAGCC |
Abbreviation: TFBS transcription factor binding sites
The table contains only statistically significant in silico predicted differentially bound transcription factors
† − The calculated log-odds scores were converted with a dynamic programming algorithm into p-values by FIMO software. The p-values for each motif occurrence were converted to q-values following Benjamini and Hochberg [38]