PKNX2.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX2.H12INVITRO.0.SM.B
Gene (human)	PKNOX2 (GeneCards)
Gene synonyms (human)	PREP2
Gene (mouse)	Pknox2
Gene synonyms (mouse)	Prep2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	15
Consensus	nndTGACAGSTGWYd
GC content	50.18%
Information content (bits; total / per base)	16.444 / 1.096
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	1519

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.995	0.993	0.984	0.978	0.964	0.951
Overall, 4 experiments	best	0.997	0.996	0.991	0.987	0.977	0.969
Methyl HT-SELEX, 2 experiments	median	0.992	0.987	0.978	0.969	0.941	0.927
Methyl HT-SELEX, 2 experiments	best	0.994	0.992	0.978	0.971	0.957	0.941
Non-Methyl HT-SELEX, 2 experiments	median	0.997	0.995	0.99	0.986	0.974	0.965
Non-Methyl HT-SELEX, 2 experiments	best	0.997	0.996	0.991	0.987	0.977	0.969

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: 3.1.4.5.2
HGNC	HGNC:16714
MGI	MGI:2445415
EntrezGene (human)	GeneID:63876 (SSTAR profile)
EntrezGene (mouse)	GeneID:208076 (SSTAR profile)
UniProt ID (human)	PKNX2_HUMAN
UniProt ID (mouse)	PKNX2_MOUSE
UniProt AC (human)	Q96KN3 (TFClass)
UniProt AC (mouse)	Q8BG99 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	PKNX2.H12INVITRO.0.SM.B.pcm
PWM	PKNX2.H12INVITRO.0.SM.B.pwm
PFM	PKNX2.H12INVITRO.0.SM.B.pfm
Alignment	PKNX2.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	PKNX2.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	PKNX2.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	PKNX2.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	PKNX2.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	PKNX2.H12INVITRO.0.SM.B_homer_format_0.001.txt PKNX2.H12INVITRO.0.SM.B_homer_format_0.0005.txt PKNX2.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	424.5	275.5	487.5	331.5
02	439.75	192.75	457.75	428.75
03	367.0	106.0	373.0	673.0
04	1.0	30.0	4.0	1484.0
05	0.0	0.0	1519.0	0.0
06	1516.0	0.0	2.0	1.0
07	0.0	1519.0	0.0	0.0
08	1519.0	0.0	0.0	0.0
09	0.0	17.0	1467.0	35.0
10	36.0	826.0	625.0	32.0
11	9.0	88.0	17.0	1405.0
12	124.0	46.0	1232.0	117.0
13	262.0	129.0	215.0	913.0
14	99.25	1050.25	166.25	203.25
15	703.25	187.25	401.25	227.25

PFM

	A	C	G	T
01	0.279	0.181	0.321	0.218
02	0.289	0.127	0.301	0.282
03	0.242	0.07	0.246	0.443
04	0.001	0.02	0.003	0.977
05	0.0	0.0	1.0	0.0
06	0.998	0.0	0.001	0.001
07	0.0	1.0	0.0	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.011	0.966	0.023
10	0.024	0.544	0.411	0.021
11	0.006	0.058	0.011	0.925
12	0.082	0.03	0.811	0.077
13	0.172	0.085	0.142	0.601
14	0.065	0.691	0.109	0.134
15	0.463	0.123	0.264	0.15

PWM

	A	C	G	T
01	0.111	-0.319	0.249	-0.135
02	0.146	-0.673	0.186	0.121
03	-0.034	-1.264	-0.018	0.57
04	-4.904	-2.484	-4.181	1.359
05	-5.339	-5.339	1.383	-5.339
06	1.381	-5.339	-4.601	-4.904
07	-5.339	1.383	-5.339	-5.339
08	1.383	-5.339	-5.339	-5.339
09	-5.339	-3.009	1.348	-2.338
10	-2.311	0.774	0.496	-2.423
11	-3.562	-1.446	-3.009	1.305
12	-1.109	-2.077	1.174	-1.167
13	-0.369	-1.07	-0.565	0.874
14	-1.328	1.014	-0.82	-0.621
15	0.614	-0.702	0.055	-0.51

Standard thresholds

P-value	Threshold
0.001	1.01391
0.0005	2.57116
0.0001	5.74581