PKNX1.H12INVIVO.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12INVIVO.1.P.B
Gene (human)	PKNOX1 (GeneCards)
Gene synonyms (human)	PREP1
Gene (mouse)	Pknox1
Gene synonyms (mouse)	Prep1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	10
Consensus	WGAbKGRCdK
GC content	52.49%
Information content (bits; total / per base)	9.127 / 0.913
Data sources	ChIP-Seq
Aligned words	957

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)	0.905	0.926	0.821	0.86	0.887	0.904	3.576	3.957	315.076	485.959
Mouse	5 (35)	0.903	0.924	0.823	0.852	0.893	0.904	3.696	3.893	352.097	496.347

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.652	0.62	0.606	0.583	0.569	0.558
Overall, 6 experiments	best	0.852	0.805	0.787	0.739	0.71	0.678
Methyl HT-SELEX, 2 experiments	median	0.626	0.605	0.587	0.572	0.557	0.55
Methyl HT-SELEX, 2 experiments	best	0.742	0.694	0.677	0.639	0.621	0.599
Non-Methyl HT-SELEX, 4 experiments	median	0.683	0.648	0.632	0.607	0.592	0.577
Non-Methyl HT-SELEX, 4 experiments	best	0.852	0.805	0.787	0.739	0.71	0.678

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.493	22.125	0.239	0.174

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.H12INVIVO.1.P.B.pcm
PWM	PKNX1.H12INVIVO.1.P.B.pwm
PFM	PKNX1.H12INVIVO.1.P.B.pfm
Alignment	PKNX1.H12INVIVO.1.P.B.words.tsv
Threshold to P-value map	PKNX1.H12INVIVO.1.P.B.thr
Motif in other formats
JASPAR format	PKNX1.H12INVIVO.1.P.B_jaspar_format.txt
MEME format	PKNX1.H12INVIVO.1.P.B_meme_format.meme
Transfac format	PKNX1.H12INVIVO.1.P.B_transfac_format.txt
Homer format	PKNX1.H12INVIVO.1.P.B_homer_format_0.001.txt PKNX1.H12INVIVO.1.P.B_homer_format_0.0005.txt PKNX1.H12INVIVO.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	121.0	107.0	112.0	617.0
02	40.0	43.0	849.0	25.0
03	911.0	12.0	28.0	6.0
04	47.0	223.0	237.0	450.0
05	85.0	56.0	156.0	660.0
06	19.0	7.0	914.0	17.0
07	556.0	5.0	392.0	4.0
08	44.0	809.0	10.0	94.0
09	505.0	61.0	273.0	118.0
10	88.0	102.0	627.0	140.0

PFM

	A	C	G	T
01	0.126	0.112	0.117	0.645
02	0.042	0.045	0.887	0.026
03	0.952	0.013	0.029	0.006
04	0.049	0.233	0.248	0.47
05	0.089	0.059	0.163	0.69
06	0.02	0.007	0.955	0.018
07	0.581	0.005	0.41	0.004
08	0.046	0.845	0.01	0.098
09	0.528	0.064	0.285	0.123
10	0.092	0.107	0.655	0.146

PWM

	A	C	G	T
01	-0.675	-0.796	-0.751	0.943
02	-1.754	-1.684	1.261	-2.199
03	1.332	-2.866	-2.093	-3.441
04	-1.599	-0.07	-0.009	0.628
05	-1.022	-1.429	-0.424	1.01
06	-2.454	-3.32	1.335	-2.555
07	0.839	-3.58	0.491	-3.741
08	-1.662	1.213	-3.024	-0.923
09	0.743	-1.346	0.131	-0.7
10	-0.988	-0.843	0.959	-0.531

Standard thresholds

P-value	Threshold
0.001	4.90872
0.0005	5.72266
0.0001	7.27654