NANOG.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NANOG.H12RSNP.0.P.B
Gene (human)	NANOG (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nanog
Gene synonyms (mouse)	Ecat4, Enk
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	18
Consensus	bbYYWTTSTbhTKbdRWd
GC content	35.41%
Information content (bits; total / per base)	11.153 / 0.62
Data sources	ChIP-Seq
Aligned words	996

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	15 (95)	0.746	0.798	0.63	0.688	0.851	0.897	3.086	3.449	91.886	137.469
Mouse	25 (160)	0.749	0.825	0.629	0.733	0.814	0.886	2.989	3.607	88.063	204.432

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Methyl HT-SELEX, 1 experiments	median	0.485	0.498	0.47	0.489	0.465	0.486
Methyl HT-SELEX, 1 experiments	best	0.485	0.498	0.47	0.489	0.465	0.486

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	6.756	5.303	0.27	0.287

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	NK-related {3.1.2} (TFClass)
TF subfamily	NANOG {3.1.2.12} (TFClass)
TFClass ID	TFClass: 3.1.2.12.1
HGNC	HGNC:20857
MGI	MGI:1919200
EntrezGene (human)	GeneID:79923 (SSTAR profile)
EntrezGene (mouse)	GeneID:71950 (SSTAR profile)
UniProt ID (human)	NANOG_HUMAN
UniProt ID (mouse)	NANOG_MOUSE
UniProt AC (human)	Q9H9S0 (TFClass)
UniProt AC (mouse)	Q80Z64 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	15 human, 25 mouse
HT-SELEX	0
Methyl-HT-SELEX	1

PCM	NANOG.H12RSNP.0.P.B.pcm
PWM	NANOG.H12RSNP.0.P.B.pwm
PFM	NANOG.H12RSNP.0.P.B.pfm
Alignment	NANOG.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	NANOG.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	NANOG.H12RSNP.0.P.B_jaspar_format.txt
MEME format	NANOG.H12RSNP.0.P.B_meme_format.meme
Transfac format	NANOG.H12RSNP.0.P.B_transfac_format.txt
Homer format	NANOG.H12RSNP.0.P.B_homer_format_0.001.txt NANOG.H12RSNP.0.P.B_homer_format_0.0005.txt NANOG.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	120.0	236.0	260.0	380.0
02	97.0	222.0	210.0	467.0
03	27.0	576.0	167.0	226.0
04	29.0	601.0	27.0	339.0
05	402.0	30.0	10.0	554.0
06	15.0	32.0	26.0	923.0
07	29.0	3.0	16.0	948.0
08	47.0	242.0	664.0	43.0
09	199.0	22.0	18.0	757.0
10	125.0	266.0	182.0	423.0
11	503.0	147.0	81.0	265.0
12	57.0	76.0	37.0	826.0
13	41.0	79.0	545.0	331.0
14	73.0	487.0	139.0	297.0
15	451.0	76.0	78.0	391.0
16	588.0	95.0	207.0	106.0
17	680.0	97.0	82.0	137.0
18	188.0	139.0	173.0	496.0

PFM

	A	C	G	T
01	0.12	0.237	0.261	0.382
02	0.097	0.223	0.211	0.469
03	0.027	0.578	0.168	0.227
04	0.029	0.603	0.027	0.34
05	0.404	0.03	0.01	0.556
06	0.015	0.032	0.026	0.927
07	0.029	0.003	0.016	0.952
08	0.047	0.243	0.667	0.043
09	0.2	0.022	0.018	0.76
10	0.126	0.267	0.183	0.425
11	0.505	0.148	0.081	0.266
12	0.057	0.076	0.037	0.829
13	0.041	0.079	0.547	0.332
14	0.073	0.489	0.14	0.298
15	0.453	0.076	0.078	0.393
16	0.59	0.095	0.208	0.106
17	0.683	0.097	0.082	0.138
18	0.189	0.14	0.174	0.498

PWM

	A	C	G	T
01	-0.723	-0.053	0.043	0.42
02	-0.932	-0.114	-0.169	0.626
03	-2.167	0.835	-0.396	-0.096
04	-2.099	0.877	-2.167	0.307
05	0.476	-2.067	-3.063	0.796
06	-2.707	-2.006	-2.202	1.305
07	-2.099	-3.971	-2.649	1.332
08	-1.638	-0.028	0.977	-1.724
09	-0.222	-2.358	-2.542	1.107
10	-0.682	0.066	-0.311	0.527
11	0.7	-0.522	-1.109	0.062
12	-1.451	-1.171	-1.868	1.194
13	-1.77	-1.133	0.78	0.283
14	-1.211	0.667	-0.578	0.175
15	0.591	-1.171	-1.146	0.449
16	0.855	-0.952	-0.183	-0.845
17	1.0	-0.932	-1.097	-0.592
18	-0.279	-0.578	-0.361	0.686

Standard thresholds

P-value	Threshold
0.001	4.46446
0.0005	5.33841
0.0001	7.15196