PAX2.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX2.H12INVIVO.0.SM.D
Gene (human)	PAX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Pax2
Gene synonyms (mouse)	Pax-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	19
Consensus	vnbYRnTSAWGCGTRWMvn
GC content	54.43%
Information content (bits; total / per base)	13.929 / 0.733
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9956

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.998	0.997	0.996	0.994	0.93	0.935
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	1.0	0.999	0.998	0.997
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	0.999	0.998	0.997
Non-Methyl HT-SELEX, 3 experiments	median	0.996	0.994	0.993	0.988	0.877	0.894
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	0.999	0.999	0.982	0.975

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.685	0.389	0.557	0.375

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	PAX2-like {3.2.2.2} (TFClass)
TFClass ID	TFClass: 3.2.2.2.1
HGNC	HGNC:8616
MGI	MGI:97486
EntrezGene (human)	GeneID:5076 (SSTAR profile)
EntrezGene (mouse)	GeneID:18504 (SSTAR profile)
UniProt ID (human)	PAX2_HUMAN
UniProt ID (mouse)	PAX2_MOUSE
UniProt AC (human)	Q02962 (TFClass)
UniProt AC (mouse)	P32114 (TFClass)
GRECO-DB-TF	yes

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

PCM	PAX2.H12INVIVO.0.SM.D.pcm
PWM	PAX2.H12INVIVO.0.SM.D.pwm
PFM	PAX2.H12INVIVO.0.SM.D.pfm
Alignment	PAX2.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	PAX2.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	PAX2.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	PAX2.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	PAX2.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	PAX2.H12INVIVO.0.SM.D_homer_format_0.001.txt PAX2.H12INVIVO.0.SM.D_homer_format_0.0005.txt PAX2.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2932.25	1173.25	5081.25	769.25
02	3519.5	1920.5	2186.5	2329.5
03	266.0	2905.0	2377.0	4408.0
04	473.0	6578.0	301.0	2604.0
05	5697.0	540.0	3559.0	160.0
06	2924.0	2580.0	2780.0	1672.0
07	43.0	2374.0	237.0	7302.0
08	467.0	5867.0	3317.0	305.0
09	8264.0	24.0	1565.0	103.0
10	6805.0	239.0	116.0	2796.0
11	13.0	1905.0	8016.0	22.0
12	26.0	9778.0	89.0	63.0
13	1681.0	44.0	8039.0	192.0
14	195.0	707.0	888.0	8166.0
15	2786.0	179.0	6190.0	801.0
16	7816.0	681.0	651.0	808.0
17	1813.0	7203.0	424.0	516.0
18	1419.75	3352.75	3936.75	1246.75
19	2860.75	2031.75	3125.75	1937.75

PFM

	A	C	G	T
01	0.295	0.118	0.51	0.077
02	0.354	0.193	0.22	0.234
03	0.027	0.292	0.239	0.443
04	0.048	0.661	0.03	0.262
05	0.572	0.054	0.357	0.016
06	0.294	0.259	0.279	0.168
07	0.004	0.238	0.024	0.733
08	0.047	0.589	0.333	0.031
09	0.83	0.002	0.157	0.01
10	0.684	0.024	0.012	0.281
11	0.001	0.191	0.805	0.002
12	0.003	0.982	0.009	0.006
13	0.169	0.004	0.807	0.019
14	0.02	0.071	0.089	0.82
15	0.28	0.018	0.622	0.08
16	0.785	0.068	0.065	0.081
17	0.182	0.723	0.043	0.052
18	0.143	0.337	0.395	0.125
19	0.287	0.204	0.314	0.195

PWM

	A	C	G	T
01	0.164	-0.751	0.713	-1.172
02	0.346	-0.259	-0.129	-0.066
03	-2.228	0.154	-0.046	0.571
04	-1.657	0.971	-2.106	0.045
05	0.828	-1.525	0.357	-2.731
06	0.161	0.036	0.11	-0.397
07	-4.007	-0.047	-2.343	1.076
08	-1.669	0.857	0.287	-2.093
09	1.199	-4.551	-0.463	-3.164
10	1.005	-2.335	-3.047	0.116
11	-5.093	-0.267	1.169	-4.63
12	-4.478	1.368	-3.306	-3.642
13	-0.392	-3.985	1.172	-2.551
14	-2.536	-1.256	-1.029	1.187
15	0.113	-2.62	0.911	-1.132
16	1.144	-1.294	-1.339	-1.123
17	-0.317	1.062	-1.765	-1.57
18	-0.561	0.298	0.458	-0.69
19	0.139	-0.203	0.228	-0.25

Standard thresholds

P-value	Threshold
0.001	3.42851
0.0005	4.53931
0.0001	6.82356