PKNX1.H12CORE.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12CORE.2.SM.B
Gene (human)	PKNOX1 (GeneCards)
Gene synonyms (human)	PREP1
Gene (mouse)	Pknox1
Gene synonyms (mouse)	Prep1
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	8
Consensus	nKGACAbn
GC content	50.69%
Information content (bits; total / per base)	8.017 / 1.002
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9604

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	5 (35)	0.674	0.772	0.54	0.626	0.659	0.779	1.602	2.031	103.0	186.119
Mouse	5 (35)	0.654	0.721	0.51	0.573	0.685	0.754	1.724	1.951	98.319	203.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.879	0.86	0.77	0.763	0.669	0.677
Overall, 6 experiments	best	0.985	0.982	0.961	0.946	0.893	0.878
Methyl HT-SELEX, 2 experiments	median	0.846	0.822	0.759	0.745	0.664	0.667
Methyl HT-SELEX, 2 experiments	best	0.957	0.942	0.896	0.872	0.768	0.764
Non-Methyl HT-SELEX, 4 experiments	median	0.892	0.879	0.798	0.796	0.705	0.713
Non-Methyl HT-SELEX, 4 experiments	best	0.985	0.982	0.961	0.946	0.893	0.878

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.736	11.803	0.168	0.148

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	TALE-type HD {3.1.4} (TFClass)
TF subfamily	PKNOX {3.1.4.5} (TFClass)
TFClass ID	TFClass: 3.1.4.5.1
HGNC	HGNC:9022
MGI	MGI:1201409
EntrezGene (human)	GeneID:5316 (SSTAR profile)
EntrezGene (mouse)	GeneID:18771 (SSTAR profile)
UniProt ID (human)	PKNX1_HUMAN
UniProt ID (mouse)	PKNX1_MOUSE
UniProt AC (human)	P55347 (TFClass)
UniProt AC (mouse)	O70477 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 5 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	PKNX1.H12CORE.2.SM.B.pcm
PWM	PKNX1.H12CORE.2.SM.B.pwm
PFM	PKNX1.H12CORE.2.SM.B.pfm
Alignment	PKNX1.H12CORE.2.SM.B.words.tsv
Threshold to P-value map	PKNX1.H12CORE.2.SM.B.thr
Motif in other formats
JASPAR format	PKNX1.H12CORE.2.SM.B_jaspar_format.txt
MEME format	PKNX1.H12CORE.2.SM.B_meme_format.meme
Transfac format	PKNX1.H12CORE.2.SM.B_transfac_format.txt
Homer format	PKNX1.H12CORE.2.SM.B_homer_format_0.001.txt PKNX1.H12CORE.2.SM.B_homer_format_0.0005.txt PKNX1.H12CORE.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1863.25	2565.25	2302.25	2873.25
02	636.5	765.5	888.5	7313.5
03	326.0	163.0	8653.0	462.0
04	9396.0	0.0	208.0	0.0
05	199.0	9366.0	39.0	0.0
06	8992.0	23.0	585.0	4.0
07	854.25	1515.25	5757.25	1477.25
08	1992.75	3224.75	2889.75	1496.75

PFM

	A	C	G	T
01	0.194	0.267	0.24	0.299
02	0.066	0.08	0.093	0.762
03	0.034	0.017	0.901	0.048
04	0.978	0.0	0.022	0.0
05	0.021	0.975	0.004	0.0
06	0.936	0.002	0.061	0.0
07	0.089	0.158	0.599	0.154
08	0.207	0.336	0.301	0.156

PWM

	A	C	G	T
01	-0.253	0.066	-0.042	0.179
02	-1.325	-1.141	-0.992	1.113
03	-1.991	-2.677	1.281	-1.644
04	1.364	-6.955	-2.436	-6.955
05	-2.48	1.36	-4.064	-6.955
06	1.32	-4.554	-1.409	-5.945
07	-1.032	-0.46	0.874	-0.485
08	-0.186	0.295	0.185	-0.472

Standard thresholds

P-value	Threshold
0.001	5.312105
0.0005	5.90127
0.0001	7.337695