NKX25.H12INVIVO.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NKX25.H12INVIVO.1.P.B
Gene (human)	NKX2-5 (GeneCards)
Gene synonyms (human)	CSX, NKX2.5, NKX2E
Gene (mouse)	Nkx2-5
Gene synonyms (mouse)	Csx, Nkx-2.5, Nkx2e
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	13
Consensus	ddSTGhTGASARv
GC content	51.4%
Information content (bits; total / per base)	10.787 / 0.83
Data sources	ChIP-Seq
Aligned words	1002

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	2 (14)	0.844	0.855	0.746	0.766	0.806	0.812	2.724	2.777	109.008	124.77
Mouse	7 (29)	0.653	0.821	0.53	0.732	0.619	0.795	1.666	2.671	15.208	79.301

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.529	0.515	0.53	0.516	0.526	0.514
Overall, 2 experiments	best	0.545	0.524	0.541	0.522	0.533	0.519
Methyl HT-SELEX, 1 experiments	median	0.513	0.507	0.518	0.509	0.518	0.509
Methyl HT-SELEX, 1 experiments	best	0.513	0.507	0.518	0.509	0.518	0.509
Non-Methyl HT-SELEX, 1 experiments	median	0.545	0.524	0.541	0.522	0.533	0.519
Non-Methyl HT-SELEX, 1 experiments	best	0.545	0.524	0.541	0.522	0.533	0.519

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	NK4 {3.1.2.17} (TFClass)
TFClass ID	TFClass: 3.1.2.17.2
HGNC	HGNC:2488
MGI	MGI:97350
EntrezGene (human)	GeneID:1482 (SSTAR profile)
EntrezGene (mouse)	GeneID:18091 (SSTAR profile)
UniProt ID (human)	NKX25_HUMAN
UniProt ID (mouse)	NKX25_MOUSE
UniProt AC (human)	P52952 (TFClass)
UniProt AC (mouse)	P42582 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 7 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	NKX25.H12INVIVO.1.P.B.pcm
PWM	NKX25.H12INVIVO.1.P.B.pwm
PFM	NKX25.H12INVIVO.1.P.B.pfm
Alignment	NKX25.H12INVIVO.1.P.B.words.tsv
Threshold to P-value map	NKX25.H12INVIVO.1.P.B.thr
Motif in other formats
JASPAR format	NKX25.H12INVIVO.1.P.B_jaspar_format.txt
MEME format	NKX25.H12INVIVO.1.P.B_meme_format.meme
Transfac format	NKX25.H12INVIVO.1.P.B_transfac_format.txt
Homer format	NKX25.H12INVIVO.1.P.B_homer_format_0.001.txt NKX25.H12INVIVO.1.P.B_homer_format_0.0005.txt NKX25.H12INVIVO.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	444.0	98.0	334.0	126.0
02	320.0	91.0	439.0	152.0
03	85.0	265.0	584.0	68.0
04	83.0	32.0	50.0	837.0
05	21.0	41.0	933.0	7.0
06	239.0	333.0	124.0	306.0
07	55.0	10.0	67.0	870.0
08	31.0	7.0	963.0	1.0
09	943.0	17.0	20.0	22.0
10	173.0	547.0	252.0	30.0
11	819.0	4.0	38.0	141.0
12	145.0	24.0	730.0	103.0
13	195.0	295.0	398.0	114.0

PFM

	A	C	G	T
01	0.443	0.098	0.333	0.126
02	0.319	0.091	0.438	0.152
03	0.085	0.264	0.583	0.068
04	0.083	0.032	0.05	0.835
05	0.021	0.041	0.931	0.007
06	0.239	0.332	0.124	0.305
07	0.055	0.01	0.067	0.868
08	0.031	0.007	0.961	0.001
09	0.941	0.017	0.02	0.022
10	0.173	0.546	0.251	0.03
11	0.817	0.004	0.038	0.141
12	0.145	0.024	0.729	0.103
13	0.195	0.294	0.397	0.114

PWM

	A	C	G	T
01	0.569	-0.928	0.286	-0.68
02	0.243	-1.001	0.558	-0.495
03	-1.068	0.056	0.843	-1.286
04	-1.091	-2.012	-1.584	1.202
05	-2.407	-1.775	1.31	-3.364
06	-0.047	0.283	-0.696	0.199
07	-1.492	-3.068	-1.3	1.24
08	-2.042	-3.364	1.342	-4.527
09	1.321	-2.6	-2.452	-2.364
10	-0.367	0.777	0.006	-2.073
11	1.18	-3.785	-1.848	-0.569
12	-0.542	-2.283	1.065	-0.879
13	-0.249	0.162	0.46	-0.779

Standard thresholds

P-value	Threshold
0.001	4.53411
0.0005	5.42071
0.0001	7.24336