NANOG.H12INVITRO.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NANOG.H12INVITRO.1.P.B
Gene (human)	NANOG (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nanog
Gene synonyms (mouse)	Ecat4, Enk
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	11
Consensus	nbTRATGGSYb
GC content	47.44%
Information content (bits; total / per base)	9.285 / 0.844
Data sources	ChIP-Seq
Aligned words	500

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)	0.666	0.709	0.489	0.531	0.579	0.631	1.284	1.463	20.276	53.62
Mouse	25 (160)	0.688	0.802	0.534	0.64	0.607	0.713	1.43	1.799	35.921	86.481

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Methyl HT-SELEX, 1 experiments	median	0.725	0.651	0.701	0.635	0.656	0.61
Methyl HT-SELEX, 1 experiments	best	0.725	0.651	0.701	0.635	0.656	0.61

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	0.609	0.689	-0.041	0.019

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.H12INVITRO.1.P.B.pcm
PWM	NANOG.H12INVITRO.1.P.B.pwm
PFM	NANOG.H12INVITRO.1.P.B.pfm
Alignment	NANOG.H12INVITRO.1.P.B.words.tsv
Threshold to P-value map	NANOG.H12INVITRO.1.P.B.thr
Motif in other formats
JASPAR format	NANOG.H12INVITRO.1.P.B_jaspar_format.txt
MEME format	NANOG.H12INVITRO.1.P.B_meme_format.meme
Transfac format	NANOG.H12INVITRO.1.P.B_transfac_format.txt
Homer format	NANOG.H12INVITRO.1.P.B_homer_format_0.001.txt NANOG.H12INVITRO.1.P.B_homer_format_0.0005.txt NANOG.H12INVITRO.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	71.0	164.0	163.0	102.0
02	42.0	145.0	86.0	227.0
03	67.0	9.0	22.0	402.0
04	182.0	5.0	313.0	0.0
05	481.0	8.0	2.0	9.0
06	12.0	3.0	7.0	478.0
07	6.0	3.0	370.0	121.0
08	48.0	7.0	432.0	13.0
09	27.0	287.0	113.0	73.0
10	22.0	157.0	19.0	302.0
11	43.0	166.0	128.0	163.0

PFM

	A	C	G	T
01	0.142	0.328	0.326	0.204
02	0.084	0.29	0.172	0.454
03	0.134	0.018	0.044	0.804
04	0.364	0.01	0.626	0.0
05	0.962	0.016	0.004	0.018
06	0.024	0.006	0.014	0.956
07	0.012	0.006	0.74	0.242
08	0.096	0.014	0.864	0.026
09	0.054	0.574	0.226	0.146
10	0.044	0.314	0.038	0.604
11	0.086	0.332	0.256	0.326

PWM

	A	C	G	T
01	-0.556	0.269	0.263	-0.201
02	-1.067	0.147	-0.368	0.591
03	-0.613	-2.484	-1.681	1.16
04	0.372	-2.961	0.91	-4.4
05	1.338	-2.584	-3.573	-2.484
06	-2.234	-3.325	-2.694	1.332
07	-2.819	-3.325	1.077	-0.032
08	-0.938	-2.694	1.231	-2.163
09	-1.489	0.824	-0.1	-0.529
10	-1.681	0.225	-1.818	0.875
11	-1.044	0.281	0.023	0.263

Standard thresholds

P-value	Threshold
0.001	4.92017
0.0005	5.739355
0.0001	7.379345