NANOG.H14RSNP.2.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NANOG.H14RSNP.2.M.C
Gene (human)	NANOG (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nanog
Gene synonyms (mouse)	Ecat4, Enk
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	12
Consensus	nRTTAAKGdddd
GC content	31.4%
Information content (bits; total / per base)	10.811 / 0.901
Data sources	Methyl-HT-SELEX
Aligned words	6689
Previous names	NANOG.H12RSNP.2.M.C

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)	0.543	0.598	0.372	0.413	0.576	0.639	1.315	1.519	8.108	26.658
Mouse	25 (160)	0.56	0.673	0.371	0.471	0.521	0.657	1.115	1.553	4.68	16.229

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Methyl HT-SELEX, 1 experiments	median	0.789	0.725	0.739	0.682	0.688	0.644
Methyl HT-SELEX, 1 experiments	best	0.789	0.725	0.739	0.682	0.688	0.644

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.384	0.332	0.101	0.053

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.H14RSNP.2.M.C.pcm
PWM	NANOG.H14RSNP.2.M.C.pwm
PFM	NANOG.H14RSNP.2.M.C.pfm
Threshold to P-value map	NANOG.H14RSNP.2.M.C.thr
Motif in other formats
JASPAR format	NANOG.H14RSNP.2.M.C_jaspar_format.txt
MEME format	NANOG.H14RSNP.2.M.C_meme_format.meme
Transfac format	NANOG.H14RSNP.2.M.C_transfac_format.txt
Homer format	NANOG.H14RSNP.2.M.C_homer_format_0.001.txt NANOG.H14RSNP.2.M.C_homer_format_0.0005.txt NANOG.H14RSNP.2.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1716.75	1019.75	1489.75	2462.75
02	1643.5	301.5	4054.5	689.5
03	370.0	102.0	644.0	5573.0
04	0.0	2.0	0.0	6687.0
05	6331.0	0.0	358.0	0.0
06	6688.0	0.0	1.0	0.0
07	1.0	862.0	1037.0	4789.0
08	2.0	8.0	5600.0	1079.0
09	3070.0	194.0	2254.0	1171.0
10	789.5	450.5	1715.5	3733.5
11	1139.5	418.5	2159.5	2971.5
12	1764.25	521.25	2015.25	2388.25

PFM

	A	C	G	T
01	0.257	0.152	0.223	0.368
02	0.246	0.045	0.606	0.103
03	0.055	0.015	0.096	0.833
04	0.0	0.0	0.0	1.0
05	0.946	0.0	0.054	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.129	0.155	0.716
08	0.0	0.001	0.837	0.161
09	0.459	0.029	0.337	0.175
10	0.118	0.067	0.256	0.558
11	0.17	0.063	0.323	0.444
12	0.264	0.078	0.301	0.357

PWM

	A	C	G	T
01	0.026	-0.494	-0.115	0.387
02	-0.017	-1.707	0.885	-0.884
03	-1.504	-2.777	-0.952	1.203
04	-6.634	-5.988	-6.634	1.385
05	1.33	-6.634	-1.537	-6.634
06	1.385	-6.634	-6.259	-6.634
07	-6.259	-0.661	-0.477	1.051
08	-5.988	-5.101	1.208	-0.437
09	0.607	-2.144	0.298	-0.356
10	-0.749	-1.308	0.026	0.802
11	-0.383	-1.381	0.255	0.574
12	0.053	-1.163	0.186	0.356

Standard thresholds

P-value	Threshold
0.001	4.64752
0.0005	5.66202
0.0001	7.493025