PKNX1.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12INVIVO.0.P.B
Gene (human)	PKNOX1 (GeneCards)
Gene synonyms (human)	PREP1
Gene (mouse)	Pknox1
Gene synonyms (mouse)	Prep1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	13
Consensus	bbbYSATTGGYhv
GC content	50.73%
Information content (bits; total / per base)	11.414 / 0.878
Data sources	ChIP-Seq
Aligned words	1000

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)	0.928	0.939	0.836	0.861	0.899	0.918	3.537	3.735	199.481	229.469
Mouse	5 (35)	0.914	0.935	0.821	0.853	0.897	0.921	3.599	3.771	191.699	234.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.531	0.523	0.521	0.515	0.516	0.511
Overall, 6 experiments	best	0.669	0.618	0.624	0.587	0.592	0.566
Methyl HT-SELEX, 2 experiments	median	0.531	0.523	0.517	0.514	0.512	0.51
Methyl HT-SELEX, 2 experiments	best	0.573	0.548	0.548	0.533	0.534	0.525
Non-Methyl HT-SELEX, 4 experiments	median	0.557	0.538	0.543	0.529	0.534	0.523
Non-Methyl HT-SELEX, 4 experiments	best	0.669	0.618	0.624	0.587	0.592	0.566

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.148	13.303	0.193	0.139

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.0.P.B.pcm
PWM	PKNX1.H12INVIVO.0.P.B.pwm
PFM	PKNX1.H12INVIVO.0.P.B.pfm
Alignment	PKNX1.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	PKNX1.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	PKNX1.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	PKNX1.H12INVIVO.0.P.B_meme_format.meme
Transfac format	PKNX1.H12INVIVO.0.P.B_transfac_format.txt
Homer format	PKNX1.H12INVIVO.0.P.B_homer_format_0.001.txt PKNX1.H12INVIVO.0.P.B_homer_format_0.0005.txt PKNX1.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	128.0	408.0	145.0	319.0
02	100.0	225.0	258.0	417.0
03	109.0	482.0	188.0	221.0
04	22.0	232.0	39.0	707.0
05	18.0	240.0	668.0	74.0
06	985.0	2.0	7.0	6.0
07	3.0	52.0	97.0	848.0
08	4.0	0.0	15.0	981.0
09	1.0	0.0	991.0	8.0
10	231.0	1.0	765.0	3.0
11	88.0	741.0	27.0	144.0
12	303.0	200.0	108.0	389.0
13	167.0	157.0	547.0	129.0

PFM

	A	C	G	T
01	0.128	0.408	0.145	0.319
02	0.1	0.225	0.258	0.417
03	0.109	0.482	0.188	0.221
04	0.022	0.232	0.039	0.707
05	0.018	0.24	0.668	0.074
06	0.985	0.002	0.007	0.006
07	0.003	0.052	0.097	0.848
08	0.004	0.0	0.015	0.981
09	0.001	0.0	0.991	0.008
10	0.231	0.001	0.765	0.003
11	0.088	0.741	0.027	0.144
12	0.303	0.2	0.108	0.389
13	0.167	0.157	0.547	0.129

PWM

	A	C	G	T
01	-0.663	0.487	-0.54	0.242
02	-0.906	-0.105	0.031	0.509
03	-0.821	0.653	-0.283	-0.122
04	-2.362	-0.074	-1.821	1.035
05	-2.546	-0.041	0.979	-1.201
06	1.366	-4.213	-3.362	-3.484
07	-3.975	-1.544	-0.936	1.217
08	-3.783	-4.982	-2.711	1.362
09	-4.525	-4.982	1.372	-3.253
10	-0.078	-4.525	1.114	-3.975
11	-1.032	1.082	-2.171	-0.547
12	0.191	-0.221	-0.83	0.44
13	-0.4	-0.461	0.779	-0.655

Standard thresholds

P-value	Threshold
0.001	4.35601
0.0005	5.390065
0.0001	7.38882