PKNX1.H12INVITRO.3.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12INVITRO.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	nnbTGACAGSKRdS
GC content	52.72%
Information content (bits; total / per base)	14.557 / 1.04
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	348

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)	0.636	0.74	0.494	0.593	0.631	0.745	1.608	2.055	96.745	164.432
Mouse	5 (35)	0.632	0.693	0.48	0.544	0.648	0.711	1.709	2.003	79.387	160.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.865	0.852	0.758	0.753	0.655	0.666
Overall, 6 experiments	best	0.99	0.988	0.95	0.935	0.861	0.847
Methyl HT-SELEX, 2 experiments	median	0.85	0.828	0.753	0.743	0.649	0.659
Methyl HT-SELEX, 2 experiments	best	0.959	0.944	0.887	0.865	0.748	0.75
Non-Methyl HT-SELEX, 4 experiments	median	0.875	0.865	0.788	0.786	0.692	0.703
Non-Methyl HT-SELEX, 4 experiments	best	0.99	0.988	0.95	0.935	0.861	0.847

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.123	8.858	0.173	0.128

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.3.SM.B.pcm
PWM	PKNX1.H12INVITRO.3.SM.B.pwm
PFM	PKNX1.H12INVITRO.3.SM.B.pfm
Alignment	PKNX1.H12INVITRO.3.SM.B.words.tsv
Threshold to P-value map	PKNX1.H12INVITRO.3.SM.B.thr
Motif in other formats
JASPAR format	PKNX1.H12INVITRO.3.SM.B_jaspar_format.txt
MEME format	PKNX1.H12INVITRO.3.SM.B_meme_format.meme
Transfac format	PKNX1.H12INVITRO.3.SM.B_transfac_format.txt
Homer format	PKNX1.H12INVITRO.3.SM.B_homer_format_0.001.txt PKNX1.H12INVITRO.3.SM.B_homer_format_0.0005.txt PKNX1.H12INVITRO.3.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	86.5	73.5	114.5	73.5
02	91.5	44.5	110.5	101.5
03	47.0	54.0	118.0	129.0
04	0.0	6.0	0.0	342.0
05	0.0	0.0	348.0	0.0
06	348.0	0.0	0.0	0.0
07	0.0	348.0	0.0	0.0
08	348.0	0.0	0.0	0.0
09	0.0	21.0	303.0	24.0
10	33.0	155.0	152.0	8.0
11	15.0	25.0	35.0	273.0
12	36.0	15.0	276.0	21.0
13	63.25	32.25	62.25	190.25
14	29.5	210.5	64.5	43.5

PFM

	A	C	G	T
01	0.249	0.211	0.329	0.211
02	0.263	0.128	0.318	0.292
03	0.135	0.155	0.339	0.371
04	0.0	0.017	0.0	0.983
05	0.0	0.0	1.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	1.0	0.0	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.06	0.871	0.069
10	0.095	0.445	0.437	0.023
11	0.043	0.072	0.101	0.784
12	0.103	0.043	0.793	0.06
13	0.182	0.093	0.179	0.547
14	0.085	0.605	0.185	0.125

PWM

	A	C	G	T
01	-0.006	-0.166	0.271	-0.166
02	0.05	-0.655	0.236	0.152
03	-0.602	-0.467	0.3	0.389
04	-4.102	-2.473	-4.102	1.356
05	-4.102	-4.102	1.374	-4.102
06	1.374	-4.102	-4.102	-4.102
07	-4.102	1.374	-4.102	-4.102
08	1.374	-4.102	-4.102	-4.102
09	-4.102	-1.371	1.236	-1.245
10	-0.943	0.57	0.551	-2.235
11	-1.681	-1.207	-0.886	1.132
12	-0.859	-1.681	1.143	-1.371
13	-0.313	-0.965	-0.328	0.773
14	-1.05	0.874	-0.293	-0.677

Standard thresholds

P-value	Threshold
0.001	2.98591
0.0005	4.24021
0.0001	6.84836