PRRX2.H12INVIVO.1.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRRX2.H12INVIVO.1.S.D
Gene (human)	PRRX2 (GeneCards)
Gene synonyms (human)	PMX2, PRX2
Gene (mouse)	Prrx2
Gene synonyms (mouse)	Prx2, S8
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	16
Consensus	nbnbTAATTARhYdRn
GC content	27.09%
Information content (bits; total / per base)	14.974 / 0.936
Data sources	HT-SELEX
Aligned words	632

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.927	0.885	0.87	0.836	0.743	0.737
Overall, 8 experiments	best	0.994	0.99	0.992	0.987	0.984	0.977
Methyl HT-SELEX, 2 experiments	median	0.956	0.926	0.926	0.899	0.881	0.859
Methyl HT-SELEX, 2 experiments	best	0.994	0.99	0.992	0.987	0.984	0.977
Non-Methyl HT-SELEX, 6 experiments	median	0.927	0.885	0.834	0.816	0.679	0.699
Non-Methyl HT-SELEX, 6 experiments	best	0.969	0.945	0.954	0.927	0.875	0.851

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.878	0.79	0.835	0.606

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	PRRX {3.1.3.21} (TFClass)
TFClass ID	TFClass: 3.1.3.21.2
HGNC	HGNC:21338
MGI	MGI:98218
EntrezGene (human)	GeneID:51450 (SSTAR profile)
EntrezGene (mouse)	GeneID:20204 (SSTAR profile)
UniProt ID (human)	PRRX2_HUMAN
UniProt ID (mouse)	PRRX2_MOUSE
UniProt AC (human)	Q99811 (TFClass)
UniProt AC (mouse)	Q06348 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	PRRX2.H12INVIVO.1.S.D.pcm
PWM	PRRX2.H12INVIVO.1.S.D.pwm
PFM	PRRX2.H12INVIVO.1.S.D.pfm
Alignment	PRRX2.H12INVIVO.1.S.D.words.tsv
Threshold to P-value map	PRRX2.H12INVIVO.1.S.D.thr
Motif in other formats
JASPAR format	PRRX2.H12INVIVO.1.S.D_jaspar_format.txt
MEME format	PRRX2.H12INVIVO.1.S.D_meme_format.meme
Transfac format	PRRX2.H12INVIVO.1.S.D_transfac_format.txt
Homer format	PRRX2.H12INVIVO.1.S.D_homer_format_0.001.txt PRRX2.H12INVIVO.1.S.D_homer_format_0.0005.txt PRRX2.H12INVIVO.1.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	116.75	163.75	162.75	188.75
02	83.0	259.0	131.0	159.0
03	174.0	137.0	231.0	90.0
04	44.0	322.0	94.0	172.0
05	0.0	2.0	0.0	630.0
06	632.0	0.0	0.0	0.0
07	632.0	0.0	0.0	0.0
08	0.0	0.0	0.0	632.0
09	0.0	0.0	0.0	632.0
10	589.0	0.0	42.0	1.0
11	348.0	16.0	267.0	1.0
12	265.0	62.0	48.0	257.0
13	18.0	83.0	48.0	483.0
14	130.0	85.0	111.0	306.0
15	412.5	64.5	108.5	46.5
16	185.25	119.25	182.25	145.25

PFM

	A	C	G	T
01	0.185	0.259	0.258	0.299
02	0.131	0.41	0.207	0.252
03	0.275	0.217	0.366	0.142
04	0.07	0.509	0.149	0.272
05	0.0	0.003	0.0	0.997
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.0	1.0
10	0.932	0.0	0.066	0.002
11	0.551	0.025	0.422	0.002
12	0.419	0.098	0.076	0.407
13	0.028	0.131	0.076	0.764
14	0.206	0.134	0.176	0.484
15	0.653	0.102	0.172	0.074
16	0.293	0.189	0.288	0.23

PWM

	A	C	G	T
01	-0.299	0.035	0.029	0.176
02	-0.635	0.49	-0.185	0.006
03	0.096	-0.141	0.377	-0.555
04	-1.253	0.707	-0.512	0.084
05	-4.595	-3.788	-4.595	1.376
06	1.379	-4.595	-4.595	-4.595
07	1.379	-4.595	-4.595	-4.595
08	-4.595	-4.595	-4.595	1.379
09	-4.595	-4.595	-4.595	1.379
10	1.308	-4.595	-1.297	-4.113
11	0.784	-2.204	0.521	-4.113
12	0.513	-0.92	-1.169	0.483
13	-2.097	-0.635	-1.169	1.111
14	-0.193	-0.611	-0.349	0.656
15	0.953	-0.881	-0.371	-1.199
16	0.158	-0.278	0.141	-0.083

Standard thresholds

P-value	Threshold
0.001	2.21976
0.0005	3.55091
0.0001	6.54461