NKX32.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NKX32.H12INVITRO.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	10
Consensus	nhTAAGTGbn
GC content	41.01%
Information content (bits; total / per base)	10.198 / 1.02
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9976

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)	0.863	0.975	0.802	0.949	0.794	0.929	2.48	3.372	229.292	419.237

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.976	0.963	0.921	0.904	0.802	0.808
Overall, 4 experiments	best	0.994	0.991	0.978	0.971	0.894	0.873
Methyl HT-SELEX, 1 experiments	median	0.93	0.897	0.848	0.816	0.726	0.719
Methyl HT-SELEX, 1 experiments	best	0.93	0.897	0.848	0.816	0.726	0.719
Non-Methyl HT-SELEX, 3 experiments	median	0.981	0.97	0.957	0.94	0.864	0.868
Non-Methyl HT-SELEX, 3 experiments	best	0.994	0.991	0.978	0.971	0.894	0.873

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.H12INVITRO.0.PSM.A.pcm
PWM	NKX32.H12INVITRO.0.PSM.A.pwm
PFM	NKX32.H12INVITRO.0.PSM.A.pfm
Alignment	NKX32.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	NKX32.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	NKX32.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	NKX32.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	NKX32.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	NKX32.H12INVITRO.0.PSM.A_homer_format_0.001.txt NKX32.H12INVITRO.0.PSM.A_homer_format_0.0005.txt NKX32.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2316.5	2585.5	3321.5	1752.5
02	1649.25	1915.25	1445.25	4966.25
03	407.0	407.0	643.0	8519.0
04	9783.0	0.0	181.0	12.0
05	9976.0	0.0	0.0	0.0
06	4.0	8.0	9918.0	46.0
07	195.0	56.0	276.0	9449.0
08	1906.0	89.0	7873.0	108.0
09	932.75	3272.75	3964.75	1805.75
10	1809.0	2526.0	2425.0	3216.0

PFM

	A	C	G	T
01	0.232	0.259	0.333	0.176
02	0.165	0.192	0.145	0.498
03	0.041	0.041	0.064	0.854
04	0.981	0.0	0.018	0.001
05	1.0	0.0	0.0	0.0
06	0.0	0.001	0.994	0.005
07	0.02	0.006	0.028	0.947
08	0.191	0.009	0.789	0.011
09	0.093	0.328	0.397	0.181
10	0.181	0.253	0.243	0.322

PWM

	A	C	G	T
01	-0.074	0.036	0.286	-0.352
02	-0.413	-0.264	-0.545	0.688
03	-1.808	-1.808	-1.353	1.228
04	1.366	-6.989	-2.611	-5.162
05	1.386	-6.989	-6.989	-6.989
06	-5.982	-5.49	1.38	-3.945
07	-2.538	-3.757	-2.194	1.331
08	-0.269	-3.308	1.149	-3.119
09	-0.982	0.272	0.463	-0.323
10	-0.321	0.013	-0.028	0.254

Standard thresholds

P-value	Threshold
0.001	4.637045
0.0005	5.685825
0.0001	7.75514