PAX2.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX2.H12INVITRO.0.SM.B
Gene (human)	PAX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Pax2
Gene synonyms (mouse)	Pax-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	19
Consensus	vnbYRnTSAWGCGTRACbn
GC content	54.68%
Information content (bits; total / per base)	15.34 / 0.807
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9987

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.998	0.997	0.996	0.994	0.928	0.934
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	0.997	0.994	0.993	0.989	0.874	0.892
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	0.687	0.39	0.555	0.37

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.H12INVITRO.0.SM.B.pcm
PWM	PAX2.H12INVITRO.0.SM.B.pwm
PFM	PAX2.H12INVITRO.0.SM.B.pfm
Alignment	PAX2.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	PAX2.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	PAX2.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	PAX2.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	PAX2.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	PAX2.H12INVITRO.0.SM.B_homer_format_0.001.txt PAX2.H12INVITRO.0.SM.B_homer_format_0.0005.txt PAX2.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2965.25	1135.25	5156.25	730.25
02	3570.5	1985.5	2201.5	2229.5
03	250.0	2939.0	2383.0	4415.0
04	444.0	6545.0	224.0	2774.0
05	5908.0	509.0	3396.0	174.0
06	2956.0	2498.0	2909.0	1624.0
07	50.0	2348.0	170.0	7419.0
08	412.0	5996.0	3360.0	219.0
09	8409.0	9.0	1486.0	83.0
10	6929.0	246.0	129.0	2683.0
11	10.0	1690.0	8273.0	14.0
12	11.0	9872.0	69.0	35.0
13	1352.0	25.0	8470.0	140.0
14	123.0	379.0	733.0	8752.0
15	2560.0	119.0	6767.0	541.0
16	8526.0	363.0	483.0	615.0
17	1392.0	8005.0	223.0	367.0
18	1150.0	3513.0	4113.0	1211.0
19	3074.0	1837.0	3191.0	1885.0

PFM

	A	C	G	T
01	0.297	0.114	0.516	0.073
02	0.358	0.199	0.22	0.223
03	0.025	0.294	0.239	0.442
04	0.044	0.655	0.022	0.278
05	0.592	0.051	0.34	0.017
06	0.296	0.25	0.291	0.163
07	0.005	0.235	0.017	0.743
08	0.041	0.6	0.336	0.022
09	0.842	0.001	0.149	0.008
10	0.694	0.025	0.013	0.269
11	0.001	0.169	0.828	0.001
12	0.001	0.988	0.007	0.004
13	0.135	0.003	0.848	0.014
14	0.012	0.038	0.073	0.876
15	0.256	0.012	0.678	0.054
16	0.854	0.036	0.048	0.062
17	0.139	0.802	0.022	0.037
18	0.115	0.352	0.412	0.121
19	0.308	0.184	0.32	0.189

PWM

	A	C	G	T
01	0.172	-0.787	0.725	-1.227
02	0.357	-0.229	-0.126	-0.113
03	-2.293	0.163	-0.047	0.57
04	-1.723	0.963	-2.402	0.105
05	0.861	-1.587	0.307	-2.651
06	0.169	0.001	0.153	-0.43
07	-3.867	-0.061	-2.674	1.088
08	-1.797	0.876	0.297	-2.424
09	1.214	-5.399	-0.518	-3.377
10	1.02	-2.309	-2.946	0.072
11	-5.314	-0.39	1.197	-5.032
12	-5.236	1.374	-3.557	-4.205
13	-0.613	-4.517	1.221	-2.866
14	-2.993	-1.88	-1.223	1.254
15	0.025	-3.025	0.996	-1.526
16	1.227	-1.923	-1.639	-1.398
17	-0.584	1.164	-2.406	-1.912
18	-0.774	0.341	0.499	-0.723
19	0.208	-0.307	0.245	-0.281

Standard thresholds

P-value	Threshold
0.001	2.70481
0.0005	3.92611
0.0001	6.44721