PRRX2.H13RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRRX2.H13RSNP.0.SM.B
Gene (human)	PRRX2 (GeneCards)
Gene synonyms (human)	PMX2, PRX2
Gene (mouse)	Prrx2
Gene synonyms (mouse)	Prx2, S8
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	15
Consensus	nnbTAATTARhKddn
GC content	27.52%
Information content (bits; total / per base)	12.895 / 0.86
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2373
Previous names	PRRX2.H12RSNP.0.SM.B

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.929	0.886	0.881	0.844	0.754	0.745
Overall, 8 experiments	best	0.994	0.99	0.992	0.987	0.985	0.978
Methyl HT-SELEX, 2 experiments	median	0.955	0.926	0.93	0.902	0.885	0.863
Methyl HT-SELEX, 2 experiments	best	0.994	0.99	0.992	0.987	0.985	0.978
Non-Methyl HT-SELEX, 6 experiments	median	0.929	0.886	0.847	0.827	0.69	0.708
Non-Methyl HT-SELEX, 6 experiments	best	0.969	0.945	0.961	0.934	0.948	0.918

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.896	0.782	0.823	0.604

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	PRRX {3.1.3.21} (TFClass)
TFClass ID	TFClass: 3.1.3.21.2
HGNC	HGNC:21338
MGI	MGI:98218
EntrezGene (human)	GeneID:51450 (SSTAR profile)
EntrezGene (mouse)	GeneID:20204 (SSTAR profile)
UniProt ID (human)	PRRX2_HUMAN
UniProt ID (mouse)	PRRX2_MOUSE
UniProt AC (human)	Q99811 (TFClass)
UniProt AC (mouse)	Q06348 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	PRRX2.H13RSNP.0.SM.B.pcm
PWM	PRRX2.H13RSNP.0.SM.B.pwm
PFM	PRRX2.H13RSNP.0.SM.B.pfm
Threshold to P-value map	PRRX2.H13RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	PRRX2.H13RSNP.0.SM.B_jaspar_format.txt
MEME format	PRRX2.H13RSNP.0.SM.B_meme_format.meme
Transfac format	PRRX2.H13RSNP.0.SM.B_transfac_format.txt
Homer format	PRRX2.H13RSNP.0.SM.B_homer_format_0.001.txt PRRX2.H13RSNP.0.SM.B_homer_format_0.0005.txt PRRX2.H13RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	416.75	729.75	517.75	708.75
02	494.0	678.0	793.0	408.0
03	219.0	1017.0	490.0	647.0
04	4.0	190.0	23.0	2156.0
05	2363.0	1.0	9.0	0.0
06	2373.0	0.0	0.0	0.0
07	0.0	0.0	0.0	2373.0
08	0.0	1.0	2.0	2370.0
09	2009.0	5.0	351.0	8.0
10	1038.0	139.0	1153.0	43.0
11	801.0	364.0	313.0	895.0
12	117.0	390.0	402.0	1464.0
13	646.0	311.0	443.0	973.0
14	1426.25	248.25	321.25	377.25
15	761.0	362.0	542.0	708.0

PFM

	A	C	G	T
01	0.176	0.308	0.218	0.299
02	0.208	0.286	0.334	0.172
03	0.092	0.429	0.206	0.273
04	0.002	0.08	0.01	0.909
05	0.996	0.0	0.004	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.001	0.999
09	0.847	0.002	0.148	0.003
10	0.437	0.059	0.486	0.018
11	0.338	0.153	0.132	0.377
12	0.049	0.164	0.169	0.617
13	0.272	0.131	0.187	0.41
14	0.601	0.105	0.135	0.159
15	0.321	0.153	0.228	0.298

PWM

	A	C	G	T
01	-0.352	0.206	-0.136	0.177
02	-0.182	0.133	0.289	-0.373
03	-0.991	0.538	-0.191	0.086
04	-4.607	-1.132	-3.172	1.288
05	1.38	-5.309	-3.996	-5.725
06	1.384	-5.725	-5.725	-5.725
07	-5.725	-5.725	-5.725	1.384
08	-5.725	-5.309	-5.017	1.383
09	1.217	-4.451	-0.523	-4.092
10	0.558	-1.441	0.663	-2.583
11	0.299	-0.486	-0.636	0.41
12	-1.61	-0.418	-0.388	0.901
13	0.085	-0.643	-0.291	0.493
14	0.875	-0.867	-0.611	-0.451
15	0.248	-0.492	-0.09	0.176

Standard thresholds

P-value	Threshold
0.001	2.95091
0.0005	4.48781
0.0001	7.41271