PKNX1.H12RSNP.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12RSNP.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	nTGACAbn
GC content	49.95%
Information content (bits; total / per base)	9.51 / 1.189
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7565

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)	0.66	0.77	0.533	0.625	0.65	0.779	1.613	2.066	100.347	182.921
Mouse	5 (35)	0.641	0.719	0.502	0.567	0.674	0.757	1.733	1.993	93.432	198.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.878	0.86	0.763	0.759	0.66	0.672
Overall, 6 experiments	best	0.986	0.982	0.96	0.945	0.888	0.873
Methyl HT-SELEX, 2 experiments	median	0.846	0.821	0.757	0.743	0.657	0.663
Methyl HT-SELEX, 2 experiments	best	0.957	0.942	0.894	0.87	0.766	0.762
Non-Methyl HT-SELEX, 4 experiments	median	0.892	0.878	0.791	0.793	0.694	0.707
Non-Methyl HT-SELEX, 4 experiments	best	0.986	0.982	0.96	0.945	0.888	0.873

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.617	13.877	0.181	0.142

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.2.SM.B.pcm
PWM	PKNX1.H12RSNP.2.SM.B.pwm
PFM	PKNX1.H12RSNP.2.SM.B.pfm
Alignment	PKNX1.H12RSNP.2.SM.B.words.tsv
Threshold to P-value map	PKNX1.H12RSNP.2.SM.B.thr
Motif in other formats
JASPAR format	PKNX1.H12RSNP.2.SM.B_jaspar_format.txt
MEME format	PKNX1.H12RSNP.2.SM.B_meme_format.meme
Transfac format	PKNX1.H12RSNP.2.SM.B_transfac_format.txt
Homer format	PKNX1.H12RSNP.2.SM.B_homer_format_0.001.txt PKNX1.H12RSNP.2.SM.B_homer_format_0.0005.txt PKNX1.H12RSNP.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1532.75	1959.75	1770.75	2301.75
02	358.0	459.0	448.0	6300.0
03	0.0	0.0	7565.0	0.0
04	7565.0	0.0	0.0	0.0
05	0.0	7565.0	0.0	0.0
06	7539.0	0.0	26.0	0.0
07	774.75	1205.75	4492.75	1091.75
08	1598.75	2379.75	2356.75	1229.75

PFM

	A	C	G	T
01	0.203	0.259	0.234	0.304
02	0.047	0.061	0.059	0.833
03	0.0	0.0	1.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	1.0	0.0	0.0
06	0.997	0.0	0.003	0.0
07	0.102	0.159	0.594	0.144
08	0.211	0.315	0.312	0.163

PWM

	A	C	G	T
01	-0.21	0.036	-0.066	0.196
02	-1.659	-1.412	-1.436	1.202
03	-6.743	-6.743	1.385	-6.743
04	1.385	-6.743	-6.743	-6.743
05	-6.743	1.385	-6.743	-6.743
06	1.382	-6.743	-4.206	-6.743
07	-0.891	-0.449	0.865	-0.549
08	-0.168	0.23	0.22	-0.43

Standard thresholds

P-value	Threshold
0.001	5.370785
0.0005	6.24651
0.0001	7.63647