Regression based predictor for p53 transactivation

BMC Bioinformatics

Table 1 Twenty-three p53-REs predicted positive by both p53MH and our algorithm

Gene	chr	p53-RE Start	p53-RE End	p53-RE_Dimer 1	p53-RE_Spacer	p53-RE_Dimer 2	Spacer Length	Ref.
*PLK2*	5	57793857	57793877	GGGCAAGTCC		AGGCATGTTT	0	[11]
*PPM1J*	1	113048061	113048081	GGGCTTGCTC		AGGCATGTTC	0	[25]
*DDB2*	11	47193105	47193126	GAACAAGCCC	T	GGGCATGTTT	1	[11]
KIAA1486	2	226209743	226209763	GAACATGCCT		GGGCTAGCCT	0	[11]
MTHFD1L	6	151220175	151220195	GGACATGCCT		GGGCATGTCC	0	[11]
PRKAG2	7	151016282	151016302	GAGCATGTCT		GAACATGTTC	0	[11]
AKAP6	14	31884451	31884471	AGACATGTTT		GGGCATGTCT	0	[25]
BIRC8	19	58490331	58490351	GGACATGCCT		GGGCATGTCT	0	[25]
APBB2	4	40721763	40721784	AAACTTGTTT	C	AGGCTAGCCC	1	[26]
TSHR	14	80618516	80618537	AAACTTGCTT	C	AAGCTAGCCC	1	[25]
DMD	X	31592231	31592252	AAACATGCTC	T	GGACTAGCCT	1	[25]
SLCO2B1	11	74540123	74540146	GAGCAAGCCT	GGG	GGACATGTTC	3	[26]
ATF3	1	210865885	210865908	AGGCAAGTCC	TCA	GAGCATGTTT	3	[11]
FRMD4A	10	14167552	14167577	AAGCTTGCTT	TCAGA	GGGCTTGCCT	5	[11]
EGFR	7	55176461	55176487	AAACATGCCT	TTCAAA	GAACTAGTTC	6	[25]
MMP2	16	54067700	54067729	AGGCAAGTCC	ATAAAGTGA	AAGCAAGTTT	9	[11]
KRT15	17	36930241	36930270	GAACATGCCC	TGTGAGCCT	GAGCATGTTC	9	[25]
DLG2	11	83032605	83032636	GAACATGTCC	ATGGCTGTCTC	AGACTTGTTT	11	[25]
NRXN3	14	78316130	78316162	AGACTTGCCC	AACTAGACATCA	AGGCATGTTT	12	[25]
FHIT	3	61206990	61207024	AAACTTGCTT	TCACTTTACTCTGT	GGACTTGCCC	14	[26]
DOCK9	13	98270727	98270761	GGGCAAGTCC	ACAGTGCAAAGTAA	AAGCAAGTTT	14	[25]
GRIN2A	16	9796860	9796894	AAACTTGCTT	TGACTTTACTCCAT	GGACTTGCCC	14	[25]
ACCN1	17	28722009	28722043	AGGCAAGTCC	GCAGTGCAAAGCGA	AAGCAAGTTT	14	[25]

These 23 top ranked REs had a p53MH score of 100 and a transactivation capability score of "4" by our algorithm. Of these, only 3 p53-REs (of genes PPM1J, DDB2 and PLK2; bold font) have been experimentally validated in previous studies.

ISSN: 1471-2105