NANOG.H12INVIVO.2.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NANOG.H12INVIVO.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	ndKTAAKGdddd
GC content	31.53%
Information content (bits; total / per base)	9.848 / 0.821
Data sources	Methyl-HT-SELEX
Aligned words	8858

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)	0.542	0.598	0.367	0.407	0.579	0.64	1.316	1.511	8.387	25.62
Mouse	25 (160)	0.563	0.676	0.368	0.471	0.522	0.658	1.118	1.554	6.222	18.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Methyl HT-SELEX, 1 experiments	median	0.788	0.724	0.738	0.681	0.688	0.643
Methyl HT-SELEX, 1 experiments	best	0.788	0.724	0.738	0.681	0.688	0.643

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.819	0.843	0.081	0.052

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.2.M.C.pcm
PWM	NANOG.H12INVIVO.2.M.C.pwm
PFM	NANOG.H12INVIVO.2.M.C.pfm
Alignment	NANOG.H12INVIVO.2.M.C.words.tsv
Threshold to P-value map	NANOG.H12INVIVO.2.M.C.thr
Motif in other formats
JASPAR format	NANOG.H12INVIVO.2.M.C_jaspar_format.txt
MEME format	NANOG.H12INVIVO.2.M.C_meme_format.meme
Transfac format	NANOG.H12INVIVO.2.M.C_transfac_format.txt
Homer format	NANOG.H12INVIVO.2.M.C_homer_format_0.001.txt NANOG.H12INVIVO.2.M.C_homer_format_0.0005.txt NANOG.H12INVIVO.2.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2406.25	1282.25	2063.25	3106.25
02	2400.5	646.5	4676.5	1134.5
03	700.5	255.5	1049.5	6852.5
04	12.0	13.0	0.0	8833.0
05	8313.0	0.0	545.0	0.0
06	8853.0	0.0	5.0	0.0
07	1.0	1386.0	1552.0	5919.0
08	20.0	38.0	6946.0	1854.0
09	3992.0	371.0	2875.0	1620.0
10	1254.75	779.75	2234.75	4588.75
11	1686.5	725.5	2688.5	3757.5
12	2362.75	806.75	2576.75	3111.75

PFM

	A	C	G	T
01	0.272	0.145	0.233	0.351
02	0.271	0.073	0.528	0.128
03	0.079	0.029	0.118	0.774
04	0.001	0.001	0.0	0.997
05	0.938	0.0	0.062	0.0
06	0.999	0.0	0.001	0.0
07	0.0	0.156	0.175	0.668
08	0.002	0.004	0.784	0.209
09	0.451	0.042	0.325	0.183
10	0.142	0.088	0.252	0.518
11	0.19	0.082	0.304	0.424
12	0.267	0.091	0.291	0.351

PWM

	A	C	G	T
01	0.083	-0.546	-0.071	0.338
02	0.081	-1.229	0.747	-0.668
03	-1.149	-2.152	-0.746	1.129
04	-5.045	-4.978	-6.883	1.383
05	1.322	-6.883	-1.399	-6.883
06	1.385	-6.883	-5.72	-6.883
07	-6.518	-0.468	-0.355	0.982
08	-4.6	-4.008	1.142	-0.177
09	0.589	-1.781	0.261	-0.312
10	-0.567	-1.042	0.009	0.728
11	-0.272	-1.114	0.194	0.528
12	0.065	-1.008	0.151	0.34

Standard thresholds

P-value	Threshold
0.001	5.02067
0.0005	5.887165
0.0001	7.43843