NRL.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NRL.H12INVIVO.0.SM.D
Gene (human)	NRL (GeneCards)
Gene synonyms (human)	D14S46E
Gene (mouse)	Nrl
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	ddhnTGCTGACdh
GC content	49.18%
Information content (bits; total / per base)	13.195 / 1.015
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9984

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.992	0.987	0.975	0.968	0.849	0.857
Overall, 5 experiments	best	0.999	0.999	0.998	0.997	0.969	0.967
Methyl HT-SELEX, 2 experiments	median	0.989	0.982	0.956	0.944	0.834	0.836
Methyl HT-SELEX, 2 experiments	best	0.995	0.992	0.975	0.968	0.849	0.857
Non-Methyl HT-SELEX, 3 experiments	median	0.992	0.987	0.978	0.969	0.901	0.893
Non-Methyl HT-SELEX, 3 experiments	best	0.999	0.999	0.998	0.997	0.969	0.967

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.93	0.744	0.927	0.641
batch 2	0.781	0.703	0.781	0.589

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.0.SM.D.pcm
PWM	NRL.H12INVIVO.0.SM.D.pwm
PFM	NRL.H12INVIVO.0.SM.D.pfm
Alignment	NRL.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	NRL.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	NRL.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	NRL.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	NRL.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	NRL.H12INVIVO.0.SM.D_homer_format_0.001.txt NRL.H12INVIVO.0.SM.D_homer_format_0.0005.txt NRL.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3933.25	1346.25	2402.25	2302.25
02	4290.5	945.5	1210.5	3537.5
03	3732.0	1395.0	1071.0	3786.0
04	3000.0	1629.0	2433.0	2922.0
05	323.0	1119.0	80.0	8462.0
06	15.0	41.0	9918.0	10.0
07	70.0	9894.0	15.0	5.0
08	1.0	16.0	6.0	9961.0
09	14.0	2.0	9684.0	284.0
10	9948.0	14.0	13.0	9.0
11	49.0	8794.0	189.0	952.0
12	1460.75	1310.75	5680.75	1531.75
13	1631.25	3037.25	1583.25	3732.25

PFM

	A	C	G	T
01	0.394	0.135	0.241	0.231
02	0.43	0.095	0.121	0.354
03	0.374	0.14	0.107	0.379
04	0.3	0.163	0.244	0.293
05	0.032	0.112	0.008	0.848
06	0.002	0.004	0.993	0.001
07	0.007	0.991	0.002	0.001
08	0.0	0.002	0.001	0.998
09	0.001	0.0	0.97	0.028
10	0.996	0.001	0.001	0.001
11	0.005	0.881	0.019	0.095
12	0.146	0.131	0.569	0.153
13	0.163	0.304	0.159	0.374

PWM

	A	C	G	T
01	0.454	-0.617	-0.038	-0.081
02	0.541	-0.969	-0.723	0.348
03	0.402	-0.581	-0.845	0.416
04	0.184	-0.426	-0.026	0.157
05	-2.039	-0.801	-3.413	1.22
06	-4.973	-4.055	1.379	-5.314
07	-3.543	1.377	-4.973	-5.835
08	-6.629	-4.916	-5.707	1.383
09	-5.032	-6.364	1.355	-2.166
10	1.382	-5.032	-5.095	-5.398
11	-3.886	1.259	-2.57	-0.962
12	-0.535	-0.643	0.822	-0.488
13	-0.425	0.196	-0.455	0.402

Standard thresholds

P-value	Threshold
0.001	2.818815
0.0005	4.209015
0.0001	7.165185