NRL.H13RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NRL.H13RSNP.1.SM.B
Gene (human)	NRL (GeneCards)
Gene synonyms (human)	D14S46E
Gene (mouse)	Nrl
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	20
Consensus	ndWWWdTGCTGACGTvWSMn
GC content	46.4%
Information content (bits; total / per base)	20.328 / 1.016
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	326
Previous names	NRL.H12RSNP.1.SM.B

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.99	0.983	0.962	0.955	0.825	0.834
Overall, 5 experiments	best	0.999	0.999	0.997	0.996	0.954	0.952
Methyl HT-SELEX, 2 experiments	median	0.984	0.977	0.935	0.922	0.807	0.809
Methyl HT-SELEX, 2 experiments	best	0.994	0.991	0.962	0.955	0.825	0.834
Non-Methyl HT-SELEX, 3 experiments	median	0.99	0.983	0.968	0.956	0.882	0.872
Non-Methyl HT-SELEX, 3 experiments	best	0.999	0.999	0.997	0.996	0.954	0.952

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.924	0.691	0.913	0.606
batch 2	0.793	0.701	0.755	0.555

TF superclass	Basic domains {1} (TFClass)
TF class	Basic leucine zipper factors (bZIP) {1.1} (TFClass)
TF family	Maf-related {1.1.3} (TFClass)
TF subfamily	Large MAF {1.1.3.1} (TFClass)
TFClass ID	TFClass: 1.1.3.1.4
HGNC	HGNC:8002
MGI	MGI:102567
EntrezGene (human)	GeneID:4901 (SSTAR profile)
EntrezGene (mouse)	GeneID:18185 (SSTAR profile)
UniProt ID (human)	NRL_HUMAN
UniProt ID (mouse)	NRL_MOUSE
UniProt AC (human)	P54845 (TFClass)
UniProt AC (mouse)	P54846 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	NRL.H13RSNP.1.SM.B.pcm
PWM	NRL.H13RSNP.1.SM.B.pwm
PFM	NRL.H13RSNP.1.SM.B.pfm
Threshold to P-value map	NRL.H13RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	NRL.H13RSNP.1.SM.B_jaspar_format.txt
MEME format	NRL.H13RSNP.1.SM.B_meme_format.meme
Transfac format	NRL.H13RSNP.1.SM.B_transfac_format.txt
Homer format	NRL.H13RSNP.1.SM.B_homer_format_0.001.txt NRL.H13RSNP.1.SM.B_homer_format_0.0005.txt NRL.H13RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	124.25	57.25	79.25	65.25
02	165.25	41.25	70.25	49.25
03	210.0	12.0	40.0	64.0
04	184.0	9.0	8.0	125.0
05	150.0	14.0	11.0	151.0
06	101.0	36.0	68.0	121.0
07	2.0	15.0	0.0	309.0
08	0.0	1.0	325.0	0.0
09	0.0	326.0	0.0	0.0
10	0.0	0.0	1.0	325.0
11	0.0	0.0	322.0	4.0
12	326.0	0.0	0.0	0.0
13	0.0	320.0	0.0	6.0
14	5.0	3.0	306.0	12.0
15	7.0	47.0	7.0	265.0
16	91.0	177.0	34.0	24.0
17	215.0	31.0	35.0	45.0
18	30.0	47.0	206.0	43.0
19	54.0	196.0	42.0	34.0
20	121.0	52.0	86.0	67.0

PFM

	A	C	G	T
01	0.381	0.176	0.243	0.2
02	0.507	0.127	0.215	0.151
03	0.644	0.037	0.123	0.196
04	0.564	0.028	0.025	0.383
05	0.46	0.043	0.034	0.463
06	0.31	0.11	0.209	0.371
07	0.006	0.046	0.0	0.948
08	0.0	0.003	0.997	0.0
09	0.0	1.0	0.0	0.0
10	0.0	0.0	0.003	0.997
11	0.0	0.0	0.988	0.012
12	1.0	0.0	0.0	0.0
13	0.0	0.982	0.0	0.018
14	0.015	0.009	0.939	0.037
15	0.021	0.144	0.021	0.813
16	0.279	0.543	0.104	0.074
17	0.66	0.095	0.107	0.138
18	0.092	0.144	0.632	0.132
19	0.166	0.601	0.129	0.104
20	0.371	0.16	0.264	0.206

PWM

	A	C	G	T
01	0.416	-0.346	-0.028	-0.218
02	0.698	-0.664	-0.146	-0.492
03	0.936	-1.819	-0.694	-0.237
04	0.805	-2.072	-2.173	0.422
05	0.602	-1.681	-1.897	0.609
06	0.211	-0.795	-0.178	0.389
07	-3.181	-1.618	-4.049	1.32
08	-4.049	-3.523	1.37	-4.049
09	-4.049	1.373	-4.049	-4.049
10	-4.049	-4.049	-3.523	1.37
11	-4.049	-4.049	1.361	-2.723
12	1.373	-4.049	-4.049	-4.049
13	-4.049	1.355	-4.049	-2.41
14	-2.555	-2.926	1.31	-1.819
15	-2.284	-0.538	-2.284	1.167
16	0.108	0.766	-0.85	-1.182
17	0.959	-0.939	-0.822	-0.58
18	-0.97	-0.538	0.917	-0.624
19	-0.403	0.867	-0.647	-0.85
20	0.389	-0.44	0.053	-0.192

Standard thresholds

P-value	Threshold
0.001	0.08571
0.0005	1.56586
0.0001	4.69406