Table 2.

p53 binding motifs detected by p53MH

GeneSequence positionSiteScore% MaxSequenceMean % input (4 h)
C12orf5−1,245 to +1,755+41125.86100.0AGACATGTCC AC AGACTTGTCT1.09
−83322.2486.0AGGCTTGTTA AAAA CGGCAAGACT0.07
+98918.6272.0CGCCATGTTG GTC AGGCAGGTCT0.29
GPX1−1,522 to +2,384+2,11621.9784.8GGGCTTGTCT TTG AAGCCAGCTG0.10
−18121.2381.9GGGCCAGACC . AGACATGCCT0.54
−70020.0677.4AGGTTTGTTG AGTGCAAA GGACTAGCTT0.34
PHLDA3−1,073 to +2,093−33921.1880.8AAGCAAGCCC AC CCCCTTGCTA0.53
+69118.5070.5GGTCAAGTTC AAGAAC CAGCAGGCCA1.48
+1,74018.5070.5CGCCATGTTG GCC AGGCTGGTCT0.23
PLK3−1,945 to +816−1,43022.1984.9TACCTTGTTT AT CTGCTTGCCT0.21
−44020.6078.9TAACATGCCC GGGCAA AAGCGAGCGC1.73
−96118.4870.8AAATTAGCCG GGTGTGATG GCGCATGCCT0.36
PRKAB1−1,112 to +1,942+6520.6980.0GTTCTTGCCG . CGGCTTGCCT0.46
+5719.5075.4CCCCTTGCGT TCTTGCCG CGGCTTGCCTn.t.
+7518.5171.6CGGCTTGCCT . GGGCAGGTAAn.t.
RABGGTA−1,041 to +1,473−2220.4979.0CCGCAAGTCC CT CCCCAAGCCT0.36
+1,17717.6568.1TGACAAGCCA GATTCTGGGAGCC AACCCTGATT0.11
+28716.1362.2CCTCTTGTGG AACGTGCA AAGCCTGTCC1.23
WIG1−808 to +1,694+1,59025.88100.0AAACAAGTCC . AGACATGCCT3.99
+81420.2078.1TACCTAGTTT GCTGAGGTGCTCC TAACCTGTTC0.82
−9619.6876.0GGGCCTGCTC CGCCAA GCACATGCGC0.34
  • NOTE: An algorithm, p53MH, was used to predict the p53 binding sites. “Sequence position” shows DNA sequences that were interrogated using p53MH; the positions are relative to the transcriptional start sites of the genes (National Center for Biotechnology Information built 33 of the human genome reference sequence). “Site” corresponds to the first base position of the predicted p53 binding site, “Score” and “% Max” are outputs from p53MH showing relative strength of the prediction. “Sequence” is that of the predicted site; a space is added in between sequence of spacer and those of the two decamer “half-sites” of p53 consensus element; a period represents no spacer in between decamers. ChIP was done using antibodies against p53 to validate the computational prediction. The sites showing largest enrichment experimentally are shown in bold. n.t., not tested due to overlapping sequences.