PKNX1.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12RSNP.0.P.B
Gene (human)	PKNOX1 (GeneCards)
Gene synonyms (human)	PREP1
Gene (mouse)	Pknox1
Gene synonyms (mouse)	Prep1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	bbYSATTGGYhv
GC content	49.75%
Information content (bits; total / per base)	11.375 / 0.948
Data sources	ChIP-Seq
Aligned words	995

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)	0.927	0.939	0.831	0.858	0.895	0.914	3.437	3.614	194.602	232.602
Mouse	5 (35)	0.913	0.935	0.82	0.853	0.898	0.92	3.572	3.76	204.796	244.06

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.551	0.533	0.532	0.522	0.52	0.516
Overall, 6 experiments	best	0.681	0.625	0.638	0.596	0.601	0.573
Methyl HT-SELEX, 2 experiments	median	0.531	0.522	0.519	0.515	0.513	0.51
Methyl HT-SELEX, 2 experiments	best	0.579	0.551	0.556	0.537	0.539	0.527
Non-Methyl HT-SELEX, 4 experiments	median	0.579	0.549	0.556	0.537	0.539	0.528
Non-Methyl HT-SELEX, 4 experiments	best	0.681	0.625	0.638	0.596	0.601	0.573

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.672	15.176	0.193	0.138

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.H12RSNP.0.P.B.pcm
PWM	PKNX1.H12RSNP.0.P.B.pwm
PFM	PKNX1.H12RSNP.0.P.B.pfm
Alignment	PKNX1.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	PKNX1.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	PKNX1.H12RSNP.0.P.B_jaspar_format.txt
MEME format	PKNX1.H12RSNP.0.P.B_meme_format.meme
Transfac format	PKNX1.H12RSNP.0.P.B_transfac_format.txt
Homer format	PKNX1.H12RSNP.0.P.B_homer_format_0.001.txt PKNX1.H12RSNP.0.P.B_homer_format_0.0005.txt PKNX1.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	74.0	221.0	241.0	459.0
02	83.0	457.0	210.0	245.0
03	22.0	189.0	40.0	744.0
04	32.0	195.0	693.0	75.0
05	982.0	4.0	7.0	2.0
06	6.0	75.0	97.0	817.0
07	14.0	3.0	16.0	962.0
08	5.0	1.0	989.0	0.0
09	227.0	6.0	760.0	2.0
10	68.0	766.0	24.0	137.0
11	293.0	198.0	92.0	412.0
12	260.0	126.0	530.0	79.0

PFM

	A	C	G	T
01	0.074	0.222	0.242	0.461
02	0.083	0.459	0.211	0.246
03	0.022	0.19	0.04	0.748
04	0.032	0.196	0.696	0.075
05	0.987	0.004	0.007	0.002
06	0.006	0.075	0.097	0.821
07	0.014	0.003	0.016	0.967
08	0.005	0.001	0.994	0.0
09	0.228	0.006	0.764	0.002
10	0.068	0.77	0.024	0.138
11	0.294	0.199	0.092	0.414
12	0.261	0.127	0.533	0.079

PWM

	A	C	G	T
01	-1.196	-0.117	-0.031	0.609
02	-1.084	0.605	-0.168	-0.015
03	-2.357	-0.273	-1.792	1.091
04	-2.005	-0.242	1.02	-1.183
05	1.368	-3.778	-3.357	-4.208
06	-3.479	-1.183	-0.931	1.184
07	-2.768	-3.97	-2.648	1.347
08	-3.617	-4.521	1.375	-4.978
09	-0.091	-3.479	1.112	-4.208
10	-1.279	1.12	-2.276	-0.591
11	0.163	-0.226	-0.983	0.502
12	0.044	-0.673	0.753	-1.132

Standard thresholds

P-value	Threshold
0.001	4.37756
0.0005	5.37801
0.0001	7.352145