Skip to main content

Table 5 Prediction of TFBS by the software FIMO for rs368234815, rs12980275, rs12979860, rs8099917, and rs4803217

From: Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study

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
  1. Abbreviation: TFBS transcription factor binding sites
  2. The table contains only statistically significant in silico predicted differentially bound transcription factors
  3. † − 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]