PAX1.H13RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX1.H13RSNP.0.SM.B
Gene (human)	PAX1 (GeneCards)
Gene synonyms (human)	HUP48
Gene (mouse)	Pax1
Gene synonyms (mouse)	Pax-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	17
Consensus	nbhRnYSAWGCGTGWMn
GC content	50.5%
Information content (bits; total / per base)	12.591 / 0.741
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	6022
Previous names	PAX1.H12RSNP.0.SM.B

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.83	0.84	0.786	0.794	0.761	0.766
Overall, 4 experiments	best	1.0	0.999	0.998	0.998	0.994	0.992
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.996	0.995	0.982	0.977
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.996	0.995	0.982	0.977
Non-Methyl HT-SELEX, 3 experiments	median	0.662	0.682	0.576	0.593	0.54	0.554
Non-Methyl HT-SELEX, 3 experiments	best	1.0	0.999	0.998	0.998	0.994	0.992

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.744	0.199	0.725	0.497

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Paired box factors {3.2} (TFClass)
TF family	PD {3.2.2} (TFClass)
TF subfamily	PAX1-like {3.2.2.1} (TFClass)
TFClass ID	TFClass: 3.2.2.1.1
HGNC	HGNC:8615
MGI	MGI:97485
EntrezGene (human)	GeneID:5075 (SSTAR profile)
EntrezGene (mouse)	GeneID:18503 (SSTAR profile)
UniProt ID (human)	PAX1_HUMAN
UniProt ID (mouse)	PAX1_MOUSE
UniProt AC (human)	P15863 (TFClass)
UniProt AC (mouse)	P09084 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	PAX1.H13RSNP.0.SM.B.pcm
PWM	PAX1.H13RSNP.0.SM.B.pwm
PFM	PAX1.H13RSNP.0.SM.B.pfm
Threshold to P-value map	PAX1.H13RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	PAX1.H13RSNP.0.SM.B_jaspar_format.txt
MEME format	PAX1.H13RSNP.0.SM.B_meme_format.meme
Transfac format	PAX1.H13RSNP.0.SM.B_transfac_format.txt
Homer format	PAX1.H13RSNP.0.SM.B_homer_format_0.001.txt PAX1.H13RSNP.0.SM.B_homer_format_0.0005.txt PAX1.H13RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1404.5	974.5	1302.5	2340.5
02	560.75	1129.75	1581.75	2749.75
03	1524.0	3032.0	258.0	1208.0
04	4428.0	379.0	744.0	471.0
05	1433.0	1525.0	1818.0	1246.0
06	361.0	1180.0	343.0	4138.0
07	475.0	3324.0	1873.0	350.0
08	4848.0	225.0	687.0	262.0
09	3308.0	245.0	269.0	2200.0
10	82.0	1102.0	4724.0	114.0
11	69.0	5865.0	46.0	42.0
12	923.0	16.0	5056.0	27.0
13	65.0	53.0	361.0	5543.0
14	1053.0	109.0	4700.0	160.0
15	4721.0	130.0	309.0	862.0
16	814.25	4146.25	442.25	619.25
17	1272.0	1582.0	2168.0	1000.0

PFM

	A	C	G	T
01	0.233	0.162	0.216	0.389
02	0.093	0.188	0.263	0.457
03	0.253	0.503	0.043	0.201
04	0.735	0.063	0.124	0.078
05	0.238	0.253	0.302	0.207
06	0.06	0.196	0.057	0.687
07	0.079	0.552	0.311	0.058
08	0.805	0.037	0.114	0.044
09	0.549	0.041	0.045	0.365
10	0.014	0.183	0.784	0.019
11	0.011	0.974	0.008	0.007
12	0.153	0.003	0.84	0.004
13	0.011	0.009	0.06	0.92
14	0.175	0.018	0.78	0.027
15	0.784	0.022	0.051	0.143
16	0.135	0.689	0.073	0.103
17	0.211	0.263	0.36	0.166

PWM

	A	C	G	T
01	-0.069	-0.434	-0.145	0.441
02	-0.985	-0.287	0.049	0.602
03	0.012	0.699	-1.757	-0.22
04	1.078	-1.375	-0.703	-1.159
05	-0.049	0.013	0.188	-0.189
06	-1.423	-0.243	-1.474	1.01
07	-1.15	0.791	0.218	-1.454
08	1.168	-1.893	-0.783	-1.742
09	0.786	-1.808	-1.716	0.379
10	-2.885	-0.311	1.143	-2.563
11	-3.053	1.359	-3.443	-3.53
12	-0.488	-4.418	1.21	-3.945
13	-3.111	-3.308	-1.423	1.302
14	-0.357	-2.607	1.137	-2.23
15	1.142	-2.434	-1.578	-0.557
16	-0.613	1.012	-1.222	-0.886
17	-0.168	0.049	0.364	-0.408

Standard thresholds

P-value	Threshold
0.001	4.00541
0.0005	4.98956
0.0001	7.02856