PKNX1.H12RSNP.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12RSNP.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	52.11%
Information content (bits; total / per base)	11.336 / 1.031
Data sources	ChIP-Seq
Aligned words	1005

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)	0.889	0.911	0.809	0.85	0.873	0.895	3.575	4.02	315.602	510.62
Mouse	5 (35)	0.891	0.91	0.807	0.843	0.884	0.896	3.842	4.057	351.569	494.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.673	0.639	0.618	0.596	0.576	0.566
Overall, 6 experiments	best	0.87	0.826	0.801	0.756	0.723	0.692
Methyl HT-SELEX, 2 experiments	median	0.651	0.625	0.604	0.586	0.567	0.559
Methyl HT-SELEX, 2 experiments	best	0.768	0.721	0.694	0.657	0.63	0.61
Non-Methyl HT-SELEX, 4 experiments	median	0.692	0.658	0.639	0.613	0.596	0.581
Non-Methyl HT-SELEX, 4 experiments	best	0.87	0.826	0.801	0.756	0.723	0.692

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	10.28	27.365	0.265	0.191

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.H12RSNP.1.P.B.pcm
PWM	PKNX1.H12RSNP.1.P.B.pwm
PFM	PKNX1.H12RSNP.1.P.B.pfm
Alignment	PKNX1.H12RSNP.1.P.B.words.tsv
Threshold to P-value map	PKNX1.H12RSNP.1.P.B.thr
Motif in other formats
JASPAR format	PKNX1.H12RSNP.1.P.B_jaspar_format.txt
MEME format	PKNX1.H12RSNP.1.P.B_meme_format.meme
Transfac format	PKNX1.H12RSNP.1.P.B_transfac_format.txt
Homer format	PKNX1.H12RSNP.1.P.B_homer_format_0.001.txt PKNX1.H12RSNP.1.P.B_homer_format_0.0005.txt PKNX1.H12RSNP.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	142.0	37.0	56.0	770.0
02	23.0	20.0	955.0	7.0
03	978.0	10.0	12.0	5.0
04	36.0	274.0	275.0	420.0
05	66.0	29.0	108.0	802.0
06	18.0	22.0	941.0	24.0
07	676.0	5.0	318.0	6.0
08	12.0	893.0	7.0	93.0
09	714.0	12.0	165.0	114.0
10	66.0	107.0	741.0	91.0
11	126.0	365.0	409.0	105.0

PFM

	A	C	G	T
01	0.141	0.037	0.056	0.766
02	0.023	0.02	0.95	0.007
03	0.973	0.01	0.012	0.005
04	0.036	0.273	0.274	0.418
05	0.066	0.029	0.107	0.798
06	0.018	0.022	0.936	0.024
07	0.673	0.005	0.316	0.006
08	0.012	0.889	0.007	0.093
09	0.71	0.012	0.164	0.113
10	0.066	0.106	0.737	0.091
11	0.125	0.363	0.407	0.104

PWM

	A	C	G	T
01	-0.565	-1.877	-1.478	1.115
02	-2.325	-2.455	1.33	-3.367
03	1.354	-3.071	-2.914	-3.627
04	-1.903	0.086	0.09	0.511
05	-1.318	-2.108	-0.835	1.156
06	-2.551	-2.367	1.315	-2.286
07	0.985	-3.627	0.234	-3.488
08	-2.914	1.263	-3.367	-0.982
09	1.04	-2.914	-0.417	-0.782
10	-1.318	-0.844	1.077	-1.004
11	-0.683	0.371	0.485	-0.863

Standard thresholds

P-value	Threshold
0.001	4.379235
0.0005	5.318775
0.0001	7.27264