PKNX1.H12CORE.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12CORE.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	11
Consensus	WGAbKGACRSv
GC content	53.41%
Information content (bits; total / per base)	11.453 / 1.041
Data sources	ChIP-Seq
Aligned words	996

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)	0.893	0.915	0.812	0.852	0.879	0.899	3.605	4.039	321.678	512.367
Mouse	5 (35)	0.896	0.915	0.813	0.847	0.89	0.901	3.866	4.074	356.721	505.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.674	0.64	0.619	0.597	0.575	0.566
Overall, 6 experiments	best	0.873	0.831	0.803	0.759	0.725	0.694
Methyl HT-SELEX, 2 experiments	median	0.651	0.625	0.603	0.586	0.566	0.559
Methyl HT-SELEX, 2 experiments	best	0.769	0.722	0.694	0.657	0.629	0.61
Non-Methyl HT-SELEX, 4 experiments	median	0.704	0.669	0.647	0.622	0.6	0.586
Non-Methyl HT-SELEX, 4 experiments	best	0.873	0.831	0.803	0.759	0.725	0.694

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	10.249	27.318	0.257	0.188

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.H12CORE.1.P.B.pcm
PWM	PKNX1.H12CORE.1.P.B.pwm
PFM	PKNX1.H12CORE.1.P.B.pfm
Alignment	PKNX1.H12CORE.1.P.B.words.tsv
Threshold to P-value map	PKNX1.H12CORE.1.P.B.thr
Motif in other formats
JASPAR format	PKNX1.H12CORE.1.P.B_jaspar_format.txt
MEME format	PKNX1.H12CORE.1.P.B_meme_format.meme
Transfac format	PKNX1.H12CORE.1.P.B_transfac_format.txt
Homer format	PKNX1.H12CORE.1.P.B_homer_format_0.001.txt PKNX1.H12CORE.1.P.B_homer_format_0.0005.txt PKNX1.H12CORE.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	133.0	57.0	71.0	735.0
02	37.0	15.0	939.0	5.0
03	980.0	7.0	5.0	4.0
04	47.0	279.0	267.0	403.0
05	82.0	34.0	118.0	762.0
06	10.0	7.0	972.0	7.0
07	655.0	3.0	332.0	6.0
08	11.0	930.0	4.0	51.0
09	672.0	22.0	181.0	121.0
10	66.0	103.0	749.0	78.0
11	143.0	356.0	401.0	96.0

PFM

	A	C	G	T
01	0.134	0.057	0.071	0.738
02	0.037	0.015	0.943	0.005
03	0.984	0.007	0.005	0.004
04	0.047	0.28	0.268	0.405
05	0.082	0.034	0.118	0.765
06	0.01	0.007	0.976	0.007
07	0.658	0.003	0.333	0.006
08	0.011	0.934	0.004	0.051
09	0.675	0.022	0.182	0.121
10	0.066	0.103	0.752	0.078
11	0.144	0.357	0.403	0.096

PWM

	A	C	G	T
01	-0.621	-1.451	-1.238	1.078
02	-1.868	-2.707	1.322	-3.618
03	1.365	-3.358	-3.618	-3.779
04	-1.638	0.113	0.069	0.479
05	-1.097	-1.948	-0.739	1.114
06	-3.063	-3.358	1.357	-3.358
07	0.963	-3.971	0.286	-3.48
08	-2.981	1.313	-3.779	-1.559
09	0.988	-2.358	-0.316	-0.714
10	-1.309	-0.873	1.097	-1.146
11	-0.55	0.355	0.474	-0.942

Standard thresholds

P-value	Threshold
0.001	4.33439
0.0005	5.30358
0.0001	7.29015