PKNX1.H12CORE.3.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12CORE.3.SM.B
Gene (human)	PKNOX1 (GeneCards)
Gene synonyms (human)	PREP1
Gene (mouse)	Pknox1
Gene synonyms (mouse)	Prep1
LOGO
LOGO (reverse complement)
Motif subtype	3
Quality	B

Motif length	14
Consensus	nndTGACAGSKKdb
GC content	52.45%
Information content (bits; total / per base)	14.736 / 1.053
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	681

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)	0.64	0.74	0.508	0.597	0.64	0.747	1.657	2.089	99.237	161.585
Mouse	5 (35)	0.63	0.691	0.487	0.547	0.653	0.708	1.75	2.032	85.119	172.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.861	0.849	0.751	0.748	0.648	0.661
Overall, 6 experiments	best	0.99	0.987	0.948	0.934	0.854	0.841
Methyl HT-SELEX, 2 experiments	median	0.845	0.825	0.743	0.736	0.642	0.654
Methyl HT-SELEX, 2 experiments	best	0.959	0.944	0.88	0.86	0.74	0.744
Non-Methyl HT-SELEX, 4 experiments	median	0.87	0.861	0.783	0.783	0.686	0.698
Non-Methyl HT-SELEX, 4 experiments	best	0.99	0.987	0.948	0.934	0.854	0.841

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.16	13.107	0.173	0.13

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.3.SM.B.pcm
PWM	PKNX1.H12CORE.3.SM.B.pwm
PFM	PKNX1.H12CORE.3.SM.B.pfm
Alignment	PKNX1.H12CORE.3.SM.B.words.tsv
Threshold to P-value map	PKNX1.H12CORE.3.SM.B.thr
Motif in other formats
JASPAR format	PKNX1.H12CORE.3.SM.B_jaspar_format.txt
MEME format	PKNX1.H12CORE.3.SM.B_meme_format.meme
Transfac format	PKNX1.H12CORE.3.SM.B_transfac_format.txt
Homer format	PKNX1.H12CORE.3.SM.B_homer_format_0.001.txt PKNX1.H12CORE.3.SM.B_homer_format_0.0005.txt PKNX1.H12CORE.3.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	163.75	147.75	228.75	140.75
02	203.25	83.25	186.25	208.25
03	111.0	80.0	251.0	239.0
04	0.0	25.0	0.0	656.0
05	0.0	0.0	681.0	0.0
06	681.0	0.0	0.0	0.0
07	0.0	680.0	1.0	0.0
08	681.0	0.0	0.0	0.0
09	0.0	18.0	622.0	41.0
10	49.0	247.0	374.0	11.0
11	19.0	56.0	68.0	538.0
12	53.0	32.0	542.0	54.0
13	129.0	61.0	111.0	380.0
14	64.5	388.5	117.5	110.5

PFM

	A	C	G	T
01	0.24	0.217	0.336	0.207
02	0.298	0.122	0.273	0.306
03	0.163	0.117	0.369	0.351
04	0.0	0.037	0.0	0.963
05	0.0	0.0	1.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.999	0.001	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.026	0.913	0.06
10	0.072	0.363	0.549	0.016
11	0.028	0.082	0.1	0.79
12	0.078	0.047	0.796	0.079
13	0.189	0.09	0.163	0.558
14	0.095	0.57	0.173	0.162

PWM

	A	C	G	T
01	-0.039	-0.14	0.293	-0.188
02	0.176	-0.706	0.089	0.2
03	-0.423	-0.745	0.385	0.336
04	-4.658	-1.865	-4.658	1.342
05	-4.658	-4.658	1.379	-4.658
06	1.379	-4.658	-4.658	-4.658
07	-4.658	1.378	-4.179	-4.658
08	1.379	-4.658	-4.658	-4.658
09	-4.658	-2.17	1.289	-1.394
10	-1.222	0.369	0.782	-2.611
11	-2.12	-1.093	-0.904	1.144
12	-1.146	-1.631	1.151	-1.128
13	-0.274	-1.01	-0.423	0.798
14	-0.955	0.82	-0.367	-0.427

Standard thresholds

P-value	Threshold
0.001	2.54731
0.0005	3.88756
0.0001	6.70766