PKNX1.H12INVITRO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12INVITRO.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	9
Consensus	nYGACAKvh
GC content	50.15%
Information content (bits; total / per base)	8.383 / 0.931
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9819

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)	0.68	0.776	0.536	0.625	0.658	0.783	1.662	2.176	111.229	202.319
Mouse	5 (35)	0.657	0.72	0.499	0.564	0.683	0.758	1.796	2.085	96.77	187.244

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.883	0.868	0.774	0.768	0.672	0.68
Overall, 6 experiments	best	0.99	0.986	0.961	0.945	0.889	0.874
Methyl HT-SELEX, 2 experiments	median	0.854	0.831	0.762	0.75	0.665	0.67
Methyl HT-SELEX, 2 experiments	best	0.963	0.948	0.901	0.878	0.771	0.768
Non-Methyl HT-SELEX, 4 experiments	median	0.893	0.881	0.802	0.802	0.708	0.717
Non-Methyl HT-SELEX, 4 experiments	best	0.99	0.986	0.961	0.945	0.889	0.874

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.842	7.898	0.156	0.133

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.H12INVITRO.2.SM.B.pcm
PWM	PKNX1.H12INVITRO.2.SM.B.pwm
PFM	PKNX1.H12INVITRO.2.SM.B.pfm
Alignment	PKNX1.H12INVITRO.2.SM.B.words.tsv
Threshold to P-value map	PKNX1.H12INVITRO.2.SM.B.thr
Motif in other formats
JASPAR format	PKNX1.H12INVITRO.2.SM.B_jaspar_format.txt
MEME format	PKNX1.H12INVITRO.2.SM.B_meme_format.meme
Transfac format	PKNX1.H12INVITRO.2.SM.B_transfac_format.txt
Homer format	PKNX1.H12INVITRO.2.SM.B_homer_format_0.001.txt PKNX1.H12INVITRO.2.SM.B_homer_format_0.0005.txt PKNX1.H12INVITRO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1990.0	2630.0	2304.0	2895.0
02	702.5	789.5	733.5	7593.5
03	231.0	207.0	9070.0	311.0
04	9519.0	86.0	204.0	10.0
05	12.0	9802.0	5.0	0.0
06	9169.0	28.0	620.0	2.0
07	762.0	1531.0	5959.0	1567.0
08	1949.25	3461.25	3051.25	1357.25
09	1833.75	2044.75	1789.75	4150.75

PFM

	A	C	G	T
01	0.203	0.268	0.235	0.295
02	0.072	0.08	0.075	0.773
03	0.024	0.021	0.924	0.032
04	0.969	0.009	0.021	0.001
05	0.001	0.998	0.001	0.0
06	0.934	0.003	0.063	0.0
07	0.078	0.156	0.607	0.16
08	0.199	0.353	0.311	0.138
09	0.187	0.208	0.182	0.423

PWM

	A	C	G	T
01	-0.21	0.069	-0.063	0.165
02	-1.249	-1.132	-1.206	1.129
03	-2.354	-2.463	1.306	-2.06
04	1.355	-3.326	-2.477	-5.297
05	-5.147	1.384	-5.819	-6.975
06	1.317	-4.396	-1.373	-6.349
07	-1.168	-0.472	0.886	-0.448
08	-0.23	0.343	0.217	-0.592
09	-0.291	-0.183	-0.316	0.525

Standard thresholds

P-value	Threshold
0.001	5.21654
0.0005	6.00077
0.0001	7.35847