HXA2.H12RSNP.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA2.H12RSNP.0.SM.D
Gene (human)	HOXA2 (GeneCards)
Gene synonyms (human)	HOX1K
Gene (mouse)	Hoxa2
Gene synonyms (mouse)	Hox-1.11, Hoxa-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nvvYTAATTASvn
GC content	39.0%
Information content (bits; total / per base)	12.662 / 0.974
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8198

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.986	0.976	0.975	0.961	0.934	0.92
Overall, 8 experiments	best	0.995	0.991	0.991	0.985	0.98	0.971
Methyl HT-SELEX, 2 experiments	median	0.992	0.986	0.985	0.977	0.967	0.955
Methyl HT-SELEX, 2 experiments	best	0.994	0.99	0.989	0.982	0.968	0.956
Non-Methyl HT-SELEX, 6 experiments	median	0.957	0.934	0.91	0.885	0.81	0.802
Non-Methyl HT-SELEX, 6 experiments	best	0.995	0.991	0.991	0.985	0.98	0.971

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	HOX2 {3.1.1.2} (TFClass)
TFClass ID	TFClass: 3.1.1.2.1
HGNC	HGNC:5103
MGI	MGI:96174
EntrezGene (human)	GeneID:3199 (SSTAR profile)
EntrezGene (mouse)	GeneID:15399 (SSTAR profile)
UniProt ID (human)	HXA2_HUMAN
UniProt ID (mouse)	HXA2_MOUSE
UniProt AC (human)	O43364 (TFClass)
UniProt AC (mouse)	P31245 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	HXA2.H12RSNP.0.SM.D.pcm
PWM	HXA2.H12RSNP.0.SM.D.pwm
PFM	HXA2.H12RSNP.0.SM.D.pfm
Alignment	HXA2.H12RSNP.0.SM.D.words.tsv
Threshold to P-value map	HXA2.H12RSNP.0.SM.D.thr
Motif in other formats
JASPAR format	HXA2.H12RSNP.0.SM.D_jaspar_format.txt
MEME format	HXA2.H12RSNP.0.SM.D_meme_format.meme
Transfac format	HXA2.H12RSNP.0.SM.D_transfac_format.txt
Homer format	HXA2.H12RSNP.0.SM.D_homer_format_0.001.txt HXA2.H12RSNP.0.SM.D_homer_format_0.0005.txt HXA2.H12RSNP.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1861.5	2557.5	1904.5	1874.5
02	1341.25	4106.25	1458.25	1292.25
03	2175.0	2721.0	2996.0	306.0
04	205.0	5450.0	600.0	1943.0
05	0.0	0.0	0.0	8198.0
06	8198.0	0.0	0.0	0.0
07	8198.0	0.0	0.0	0.0
08	0.0	0.0	0.0	8198.0
09	0.0	92.0	1784.0	6322.0
10	7558.0	8.0	612.0	20.0
11	420.0	5246.0	1775.0	757.0
12	1310.25	3297.25	2470.25	1120.25
13	1791.5	2737.5	1752.5	1916.5

PFM

	A	C	G	T
01	0.227	0.312	0.232	0.229
02	0.164	0.501	0.178	0.158
03	0.265	0.332	0.365	0.037
04	0.025	0.665	0.073	0.237
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.011	0.218	0.771
10	0.922	0.001	0.075	0.002
11	0.051	0.64	0.217	0.092
12	0.16	0.402	0.301	0.137
13	0.219	0.334	0.214	0.234

PWM

	A	C	G	T
01	-0.096	0.221	-0.073	-0.089
02	-0.423	0.694	-0.34	-0.461
03	0.059	0.283	0.379	-1.896
04	-2.293	0.977	-1.226	-0.053
05	-6.814	-6.814	-6.814	1.385
06	1.385	-6.814	-6.814	-6.814
07	1.385	-6.814	-6.814	-6.814
08	-6.814	-6.814	-6.814	1.385
09	-6.814	-3.08	-0.139	1.126
10	1.304	-5.299	-1.206	-4.524
11	-1.581	0.939	-0.144	-0.994
12	-0.447	0.475	0.187	-0.603
13	-0.134	0.289	-0.156	-0.067

Standard thresholds

P-value	Threshold
0.001	2.43861
0.0005	4.55761
0.0001	7.564425