NRL.H12INVIVO.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NRL.H12INVIVO.1.SM.D
Gene (human)	NRL (GeneCards)
Gene synonyms (human)	D14S46E
Gene (mouse)	Nrl
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	19
Consensus	ndWWWdTGCTGACGTMRKv
GC content	46.29%
Information content (bits; total / per base)	21.187 / 1.115
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	576

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.99	0.984	0.962	0.955	0.827	0.835
Overall, 5 experiments	best	0.999	0.999	0.997	0.996	0.956	0.954
Methyl HT-SELEX, 2 experiments	median	0.984	0.976	0.938	0.925	0.812	0.813
Methyl HT-SELEX, 2 experiments	best	0.994	0.991	0.962	0.955	0.827	0.835
Non-Methyl HT-SELEX, 3 experiments	median	0.99	0.984	0.968	0.957	0.885	0.875
Non-Methyl HT-SELEX, 3 experiments	best	0.999	0.999	0.997	0.996	0.956	0.954

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.925	0.683	0.912	0.601
batch 2	0.793	0.691	0.755	0.551

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

PCM	NRL.H12INVIVO.1.SM.D.pcm
PWM	NRL.H12INVIVO.1.SM.D.pwm
PFM	NRL.H12INVIVO.1.SM.D.pfm
Alignment	NRL.H12INVIVO.1.SM.D.words.tsv
Threshold to P-value map	NRL.H12INVIVO.1.SM.D.thr
Motif in other formats
JASPAR format	NRL.H12INVIVO.1.SM.D_jaspar_format.txt
MEME format	NRL.H12INVIVO.1.SM.D_meme_format.meme
Transfac format	NRL.H12INVIVO.1.SM.D_transfac_format.txt
Homer format	NRL.H12INVIVO.1.SM.D_homer_format_0.001.txt NRL.H12INVIVO.1.SM.D_homer_format_0.0005.txt NRL.H12INVIVO.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	189.75	127.75	140.75	117.75
02	307.25	73.25	104.25	91.25
03	402.0	25.0	42.0	107.0
04	350.0	12.0	21.0	193.0
05	276.0	17.0	12.0	271.0
06	174.0	67.0	107.0	228.0
07	3.0	19.0	2.0	552.0
08	0.0	0.0	576.0	0.0
09	0.0	576.0	0.0	0.0
10	0.0	0.0	0.0	576.0
11	0.0	0.0	574.0	2.0
12	576.0	0.0	0.0	0.0
13	0.0	574.0	0.0	2.0
14	9.0	1.0	558.0	8.0
15	10.0	60.0	14.0	492.0
16	137.0	335.0	46.0	58.0
17	411.0	41.0	68.0	56.0
18	49.25	81.25	356.25	89.25
19	89.25	333.25	102.25	51.25

PFM

	A	C	G	T
01	0.329	0.222	0.244	0.204
02	0.533	0.127	0.181	0.158
03	0.698	0.043	0.073	0.186
04	0.608	0.021	0.036	0.335
05	0.479	0.03	0.021	0.47
06	0.302	0.116	0.186	0.396
07	0.005	0.033	0.003	0.958
08	0.0	0.0	1.0	0.0
09	0.0	1.0	0.0	0.0
10	0.0	0.0	0.0	1.0
11	0.0	0.0	0.997	0.003
12	1.0	0.0	0.0	0.0
13	0.0	0.997	0.0	0.003
14	0.016	0.002	0.969	0.014
15	0.017	0.104	0.024	0.854
16	0.238	0.582	0.08	0.101
17	0.714	0.071	0.118	0.097
18	0.086	0.141	0.618	0.155
19	0.155	0.579	0.178	0.089

PWM

	A	C	G	T
01	0.273	-0.118	-0.023	-0.199
02	0.752	-0.665	-0.319	-0.45
03	1.02	-1.7	-1.206	-0.293
04	0.882	-2.372	-1.863	0.29
05	0.645	-2.058	-2.372	0.627
06	0.187	-0.753	-0.293	0.456
07	-3.457	-1.956	-3.703	1.336
08	-4.518	-4.518	1.378	-4.518
09	-4.518	1.378	-4.518	-4.518
10	-4.518	-4.518	-4.518	1.378
11	-4.518	-4.518	1.375	-3.703
12	1.378	-4.518	-4.518	-4.518
13	-4.518	1.375	-4.518	-3.703
14	-2.621	-4.03	1.346	-2.72
15	-2.531	-0.86	-2.234	1.221
16	-0.049	0.838	-1.118	-0.893
17	1.042	-1.229	-0.738	-0.927
18	-1.052	-0.564	0.899	-0.472
19	-0.472	0.833	-0.338	-1.014

Standard thresholds

P-value	Threshold
0.001	-1.35859
0.0005	0.28111
0.0001	3.74796