NANOG.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NANOG.H12INVIVO.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	17
Consensus	nbYWTTSWnWTGYWRWd
GC content	35.59%
Information content (bits; total / per base)	11.886 / 0.699
Data sources	ChIP-Seq
Aligned words	999

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)	0.804	0.855	0.732	0.783	0.853	0.895	3.481	3.837	105.456	150.187
Mouse	25 (160)	0.766	0.857	0.692	0.797	0.782	0.866	3.0	3.724	80.261	183.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Methyl HT-SELEX, 1 experiments	median	0.517	0.514	0.492	0.502	0.481	0.496
Methyl HT-SELEX, 1 experiments	best	0.517	0.514	0.492	0.502	0.481	0.496

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	11.214	7.201	0.24	0.269

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.H12INVIVO.0.P.B.pcm
PWM	NANOG.H12INVIVO.0.P.B.pwm
PFM	NANOG.H12INVIVO.0.P.B.pfm
Alignment	NANOG.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	NANOG.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	NANOG.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	NANOG.H12INVIVO.0.P.B_meme_format.meme
Transfac format	NANOG.H12INVIVO.0.P.B_transfac_format.txt
Homer format	NANOG.H12INVIVO.0.P.B_homer_format_0.001.txt NANOG.H12INVIVO.0.P.B_homer_format_0.0005.txt NANOG.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	129.0	241.0	308.0	321.0
02	36.0	516.0	205.0	242.0
03	83.0	541.0	64.0	311.0
04	345.0	54.0	51.0	549.0
05	18.0	61.0	45.0	875.0
06	62.0	9.0	31.0	897.0
07	79.0	287.0	583.0	50.0
08	386.0	26.0	31.0	556.0
09	211.0	254.0	201.0	333.0
10	755.0	36.0	70.0	138.0
11	76.0	12.0	54.0	857.0
12	15.0	21.0	812.0	151.0
13	36.0	613.0	116.0	234.0
14	679.0	19.0	13.0	288.0
15	623.0	62.0	264.0	50.0
16	791.0	56.0	60.0	92.0
17	131.0	126.0	202.0	540.0

PFM

	A	C	G	T
01	0.129	0.241	0.308	0.321
02	0.036	0.517	0.205	0.242
03	0.083	0.542	0.064	0.311
04	0.345	0.054	0.051	0.55
05	0.018	0.061	0.045	0.876
06	0.062	0.009	0.031	0.898
07	0.079	0.287	0.584	0.05
08	0.386	0.026	0.031	0.557
09	0.211	0.254	0.201	0.333
10	0.756	0.036	0.07	0.138
11	0.076	0.012	0.054	0.858
12	0.015	0.021	0.813	0.151
13	0.036	0.614	0.116	0.234
14	0.68	0.019	0.013	0.288
15	0.624	0.062	0.264	0.05
16	0.792	0.056	0.06	0.092
17	0.131	0.126	0.202	0.541

PWM

	A	C	G	T
01	-0.654	-0.035	0.208	0.249
02	-1.897	0.722	-0.196	-0.031
03	-1.088	0.769	-1.342	0.218
04	0.321	-1.507	-1.562	0.784
05	-2.545	-1.389	-1.683	1.249
06	-1.373	-3.155	-2.039	1.274
07	-1.136	0.138	0.844	-1.581
08	0.433	-2.205	-2.039	0.797
09	-0.167	0.017	-0.215	0.286
10	1.102	-1.897	-1.254	-0.588
11	-1.174	-2.908	-1.507	1.228
12	-2.71	-2.404	1.174	-0.499
13	-1.897	0.894	-0.759	-0.065
14	0.996	-2.496	-2.838	0.142
15	0.91	-1.373	0.055	-1.581
16	1.148	-1.472	-1.405	-0.987
17	-0.639	-0.677	-0.211	0.767

Standard thresholds

P-value	Threshold
0.001	4.27696
0.0005	5.17741
0.0001	7.06651