PAX9.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX9.H12INVIVO.0.SM.D
Gene (human)	PAX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Pax9
Gene synonyms (mouse)	Pax-9
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	17
Consensus	bMRnYSAWGCGTGACSv
GC content	57.81%
Information content (bits; total / per base)	16.35 / 0.962
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8845

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.86	0.869	0.8	0.811	0.771	0.78
Overall, 4 experiments	best	1.0	1.0	1.0	0.999	0.998	0.997
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.999	0.999	0.991	0.989
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.999	0.999	0.991	0.989
Non-Methyl HT-SELEX, 3 experiments	median	0.72	0.739	0.6	0.623	0.552	0.571
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	0.999	0.998	0.997

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.722	0.155	0.557	0.367

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.H12INVIVO.0.SM.D.pcm
PWM	PAX9.H12INVIVO.0.SM.D.pwm
PFM	PAX9.H12INVIVO.0.SM.D.pfm
Alignment	PAX9.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	PAX9.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	PAX9.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	PAX9.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	PAX9.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	PAX9.H12INVIVO.0.SM.D_homer_format_0.001.txt PAX9.H12INVIVO.0.SM.D_homer_format_0.0005.txt PAX9.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	495.0	2527.0	2705.0	3118.0
02	1663.25	5532.25	339.25	1310.25
03	5655.0	959.0	1861.0	370.0
04	1847.0	2009.0	3179.0	1810.0
05	109.0	1852.0	376.0	6508.0
06	355.0	4957.0	3217.0	316.0
07	7224.0	39.0	1386.0	196.0
08	5956.0	345.0	239.0	2305.0
09	5.0	1432.0	7402.0	6.0
10	2.0	8832.0	6.0	5.0
11	686.0	4.0	8136.0	19.0
12	22.0	15.0	260.0	8548.0
13	1349.0	57.0	7333.0	106.0
14	8148.0	106.0	315.0	276.0
15	720.0	7833.0	142.0	150.0
16	505.25	2293.25	5358.25	688.25
17	1736.25	1768.25	4107.25	1233.25

PFM

	A	C	G	T
01	0.056	0.286	0.306	0.353
02	0.188	0.625	0.038	0.148
03	0.639	0.108	0.21	0.042
04	0.209	0.227	0.359	0.205
05	0.012	0.209	0.043	0.736
06	0.04	0.56	0.364	0.036
07	0.817	0.004	0.157	0.022
08	0.673	0.039	0.027	0.261
09	0.001	0.162	0.837	0.001
10	0.0	0.999	0.001	0.001
11	0.078	0.0	0.92	0.002
12	0.002	0.002	0.029	0.966
13	0.153	0.006	0.829	0.012
14	0.921	0.012	0.036	0.031
15	0.081	0.886	0.016	0.017
16	0.057	0.259	0.606	0.078
17	0.196	0.2	0.464	0.139

PWM

	A	C	G	T
01	-1.493	0.133	0.201	0.343
02	-0.284	0.916	-1.869	-0.523
03	0.938	-0.834	-0.172	-1.783
04	-0.18	-0.096	0.363	-0.2
05	-2.99	-0.177	-1.767	1.079
06	-1.824	0.807	0.375	-1.939
07	1.183	-3.982	-0.467	-2.413
08	0.99	-1.852	-2.216	0.041
09	-5.718	-0.434	1.207	-5.589
10	-6.25	1.384	-5.589	-5.718
11	-1.168	-5.866	1.302	-4.645
12	-4.513	-4.853	-2.133	1.351
13	-0.494	-3.62	1.198	-3.018
14	1.303	-3.018	-1.943	-2.074
15	-1.12	1.264	-2.731	-2.677
16	-1.473	0.036	0.884	-1.165
17	-0.242	-0.223	0.619	-0.583

Standard thresholds

P-value	Threshold
0.001	1.94466
0.0005	3.29861
0.0001	6.07801