NKX32.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NKX32.H12INVIVO.0.PSM.A
Gene (human)	NKX3-2 (GeneCards)
Gene synonyms (human)	BAPX1, NKX3B
Gene (mouse)	Nkx3-2
Gene synonyms (mouse)	Bapx1, Nkx-3.2, Nkx3b
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	bWRAGTGbh
GC content	39.14%
Information content (bits; total / per base)	8.852 / 0.984
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1237

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
Mouse	2 (13)	0.869	0.976	0.811	0.951	0.801	0.931	2.555	3.471	240.137	419.509

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.969	0.951	0.91	0.888	0.799	0.802
Overall, 4 experiments	best	0.991	0.984	0.974	0.964	0.888	0.861
Methyl HT-SELEX, 1 experiments	median	0.914	0.874	0.833	0.796	0.722	0.709
Methyl HT-SELEX, 1 experiments	best	0.914	0.874	0.833	0.796	0.722	0.709
Non-Methyl HT-SELEX, 3 experiments	median	0.976	0.959	0.942	0.918	0.859	0.861
Non-Methyl HT-SELEX, 3 experiments	best	0.991	0.984	0.974	0.964	0.888	0.861

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	NK3 {3.1.2.16} (TFClass)
TFClass ID	TFClass: 3.1.2.16.2
HGNC	HGNC:951
MGI	MGI:108015
EntrezGene (human)	GeneID:579 (SSTAR profile)
EntrezGene (mouse)	GeneID:12020 (SSTAR profile)
UniProt ID (human)	NKX32_HUMAN
UniProt ID (mouse)	NKX32_MOUSE
UniProt AC (human)	P78367 (TFClass)
UniProt AC (mouse)	P97503 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	NKX32.H12INVIVO.0.PSM.A.pcm
PWM	NKX32.H12INVIVO.0.PSM.A.pwm
PFM	NKX32.H12INVIVO.0.PSM.A.pfm
Alignment	NKX32.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	NKX32.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	NKX32.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	NKX32.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	NKX32.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	NKX32.H12INVIVO.0.PSM.A_homer_format_0.001.txt NKX32.H12INVIVO.0.PSM.A_homer_format_0.0005.txt NKX32.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	154.0	238.0	168.0	677.0
02	134.0	54.0	63.0	986.0
03	946.0	57.0	222.0	12.0
04	1196.0	6.0	23.0	12.0
05	20.0	12.0	1192.0	13.0
06	62.0	7.0	47.0	1121.0
07	101.0	12.0	1110.0	14.0
08	102.0	372.0	358.0	405.0
09	290.0	240.0	176.0	531.0

PFM

	A	C	G	T
01	0.124	0.192	0.136	0.547
02	0.108	0.044	0.051	0.797
03	0.765	0.046	0.179	0.01
04	0.967	0.005	0.019	0.01
05	0.016	0.01	0.964	0.011
06	0.05	0.006	0.038	0.906
07	0.082	0.01	0.897	0.011
08	0.082	0.301	0.289	0.327
09	0.234	0.194	0.142	0.429

PWM

	A	C	G	T
01	-0.691	-0.26	-0.605	0.78
02	-0.829	-1.718	-1.569	1.156
03	1.114	-1.666	-0.329	-3.117
04	1.348	-3.688	-2.53	-3.117
05	-2.659	-3.117	1.345	-3.047
06	-1.584	-3.567	-1.853	1.284
07	-1.107	-3.117	1.274	-2.981
08	-1.098	0.184	0.146	0.268
09	-0.064	-0.252	-0.559	0.538

Standard thresholds

P-value	Threshold
0.001	4.955345
0.0005	5.688685
0.0001	7.367885