PAX9.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX9.H12RSNP.0.SM.B
Gene (human)	PAX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Pax9
Gene synonyms (mouse)	Pax-9
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	20
Consensus	ndnbMRnTSAAGCGTGACbv
GC content	54.73%
Information content (bits; total / per base)	18.339 / 0.917
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	466

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.814	0.816	0.786	0.786	0.769	0.77
Overall, 4 experiments	best	1.0	1.0	0.999	0.999	0.994	0.993
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.999	0.999	0.994	0.993
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.999	0.999	0.994	0.993
Non-Methyl HT-SELEX, 3 experiments	median	0.629	0.633	0.573	0.574	0.545	0.546
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	0.999	0.999	0.994	0.993

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.696	0.168	0.596	0.408

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Paired box factors {3.2} (TFClass)
TF family	PD {3.2.2} (TFClass)
TF subfamily	PAX1-like {3.2.2.1} (TFClass)
TFClass ID	TFClass: 3.2.2.1.2
HGNC	HGNC:8623
MGI	MGI:97493
EntrezGene (human)	GeneID:5083 (SSTAR profile)
EntrezGene (mouse)	GeneID:18511 (SSTAR profile)
UniProt ID (human)	PAX9_HUMAN
UniProt ID (mouse)	PAX9_MOUSE
UniProt AC (human)	P55771 (TFClass)
UniProt AC (mouse)	P47242 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	PAX9.H12RSNP.0.SM.B.pcm
PWM	PAX9.H12RSNP.0.SM.B.pwm
PFM	PAX9.H12RSNP.0.SM.B.pfm
Alignment	PAX9.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	PAX9.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	PAX9.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	PAX9.H12RSNP.0.SM.B_meme_format.meme
Transfac format	PAX9.H12RSNP.0.SM.B_transfac_format.txt
Homer format	PAX9.H12RSNP.0.SM.B_homer_format_0.001.txt PAX9.H12RSNP.0.SM.B_homer_format_0.0005.txt PAX9.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	110.25	146.25	80.25	129.25
02	160.5	59.5	180.5	65.5
03	150.0	71.0	113.0	132.0
04	13.0	113.0	120.0	220.0
05	83.0	306.0	16.0	61.0
06	263.0	37.0	152.0	14.0
07	99.0	102.0	175.0	90.0
08	6.0	60.0	15.0	385.0
09	5.0	312.0	124.0	25.0
10	426.0	2.0	32.0	6.0
11	362.0	6.0	5.0	93.0
12	0.0	53.0	413.0	0.0
13	0.0	465.0	1.0	0.0
14	25.0	0.0	441.0	0.0
15	0.0	5.0	11.0	450.0
16	48.0	2.0	410.0	6.0
17	457.0	3.0	3.0	3.0
18	50.0	407.0	3.0	6.0
19	34.25	241.25	145.25	45.25
20	115.25	85.25	184.25	81.25

PFM

	A	C	G	T
01	0.237	0.314	0.172	0.277
02	0.344	0.128	0.387	0.141
03	0.322	0.152	0.242	0.283
04	0.028	0.242	0.258	0.472
05	0.178	0.657	0.034	0.131
06	0.564	0.079	0.326	0.03
07	0.212	0.219	0.376	0.193
08	0.013	0.129	0.032	0.826
09	0.011	0.67	0.266	0.054
10	0.914	0.004	0.069	0.013
11	0.777	0.013	0.011	0.2
12	0.0	0.114	0.886	0.0
13	0.0	0.998	0.002	0.0
14	0.054	0.0	0.946	0.0
15	0.0	0.011	0.024	0.966
16	0.103	0.004	0.88	0.013
17	0.981	0.006	0.006	0.006
18	0.107	0.873	0.006	0.013
19	0.073	0.518	0.312	0.097
20	0.247	0.183	0.395	0.174

PWM

	A	C	G	T
01	-0.054	0.225	-0.367	0.103
02	0.317	-0.66	0.433	-0.566
03	0.25	-0.487	-0.03	0.123
04	-2.094	-0.03	0.029	0.63
05	-0.334	0.958	-1.907	-0.635
06	0.807	-1.119	0.263	-2.028
07	-0.16	-0.131	0.403	-0.254
08	-2.751	-0.651	-1.965	1.186
09	-2.894	0.977	0.062	-1.492
10	1.287	-3.508	-1.258	-2.751
11	1.125	-2.751	-2.894	-0.222
12	-4.342	-0.772	1.256	-4.342
13	-4.342	1.374	-3.84	-4.342
14	-1.492	-4.342	1.322	-4.342
15	-4.342	-2.894	-2.242	1.342
16	-0.868	-3.508	1.249	-2.751
17	1.357	-3.259	-3.259	-3.259
18	-0.829	1.242	-3.259	-2.751
19	-1.193	0.721	0.218	-0.925
20	-0.011	-0.308	0.454	-0.355

Standard thresholds

P-value	Threshold
0.001	1.34376
0.0005	2.70001
0.0001	5.54906