NANOG.H13RSNP.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NANOG.H13RSNP.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	bTSWKKKYYhh
GC content	43.4%
Information content (bits; total / per base)	6.824 / 0.62
Data sources	ChIP-Seq
Aligned words	998
Previous names	NANOG.H12RSNP.1.P.B

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)	0.599	0.637	0.427	0.478	0.571	0.596	1.253	1.351	12.538	33.328
Mouse	25 (160)	0.604	0.681	0.438	0.529	0.584	0.661	1.309	1.615	17.404	76.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Methyl HT-SELEX, 1 experiments	median	0.599	0.561	0.574	0.547	0.551	0.536
Methyl HT-SELEX, 1 experiments	best	0.599	0.561	0.574	0.547	0.551	0.536

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.556	0.561	0.025	0.022

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	NANOG.H13RSNP.1.P.B.pcm
PWM	NANOG.H13RSNP.1.P.B.pwm
PFM	NANOG.H13RSNP.1.P.B.pfm
Threshold to P-value map	NANOG.H13RSNP.1.P.B.thr
Motif in other formats
JASPAR format	NANOG.H13RSNP.1.P.B_jaspar_format.txt
MEME format	NANOG.H13RSNP.1.P.B_meme_format.meme
Transfac format	NANOG.H13RSNP.1.P.B_transfac_format.txt
Homer format	NANOG.H13RSNP.1.P.B_homer_format_0.001.txt NANOG.H13RSNP.1.P.B_homer_format_0.0005.txt NANOG.H13RSNP.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	47.0	291.0	198.0	462.0
02	93.0	16.0	73.0	816.0
03	122.0	234.0	633.0	9.0
04	758.0	49.0	20.0	171.0
05	28.0	20.0	261.0	689.0
06	36.0	25.0	327.0	610.0
07	89.0	77.0	689.0	143.0
08	24.0	521.0	185.0	268.0
09	30.0	355.0	10.0	603.0
10	150.0	347.0	117.0	384.0
11	215.0	236.0	80.0	467.0

PFM

	A	C	G	T
01	0.047	0.292	0.198	0.463
02	0.093	0.016	0.073	0.818
03	0.122	0.234	0.634	0.009
04	0.76	0.049	0.02	0.171
05	0.028	0.02	0.262	0.69
06	0.036	0.025	0.328	0.611
07	0.089	0.077	0.69	0.143
08	0.024	0.522	0.185	0.269
09	0.03	0.356	0.01	0.604
10	0.15	0.348	0.117	0.385
11	0.215	0.236	0.08	0.468

PWM

	A	C	G	T
01	-1.64	0.153	-0.229	0.613
02	-0.975	-2.651	-1.213	1.18
03	-0.708	-0.064	0.927	-3.154
04	1.107	-1.6	-2.448	-0.375
05	-2.134	-2.448	0.045	1.011
06	-1.896	-2.241	0.269	0.89
07	-1.019	-1.16	1.011	-0.552
08	-2.279	0.733	-0.297	0.071
09	-2.069	0.351	-3.065	0.878
10	-0.504	0.328	-0.75	0.429
11	-0.148	-0.055	-1.123	0.624

Standard thresholds

P-value	Threshold
0.001	5.03765
0.0005	5.632415
0.0001	6.825645