RARG.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARG.H12RSNP.1.PSM.A
Gene (human)	RARG (GeneCards)
Gene synonyms (human)	NR1B3
Gene (mouse)	Rarg
Gene synonyms (mouse)	Nr1b3
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	12
Consensus	ndvAGGTCAhvn
GC content	49.02%
Information content (bits; total / per base)	12.504 / 1.042
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	346

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	5 (21)	0.723	0.794	0.563	0.632	0.692	0.765	1.812	2.045	54.796	88.585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.93	0.902	0.777	0.772	0.652	0.669
Overall, 10 experiments	best	0.998	0.997	0.997	0.994	0.993	0.99
Methyl HT-SELEX, 2 experiments	median	0.984	0.972	0.976	0.961	0.959	0.941
Methyl HT-SELEX, 2 experiments	best	0.997	0.994	0.995	0.991	0.99	0.984
Non-Methyl HT-SELEX, 8 experiments	median	0.884	0.854	0.717	0.719	0.613	0.633
Non-Methyl HT-SELEX, 8 experiments	best	0.998	0.997	0.997	0.994	0.993	0.99

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.995	0.149	0.991	0.489
batch 2	0.615	0.133	0.533	0.378

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	Thyroid hormone receptor-related {2.1.2} (TFClass)
TF subfamily	RAR (NR1B) {2.1.2.1} (TFClass)
TFClass ID	TFClass: 2.1.2.1.3
HGNC	HGNC:9866
MGI	MGI:97858
EntrezGene (human)	GeneID:5916 (SSTAR profile)
EntrezGene (mouse)	GeneID:19411 (SSTAR profile)
UniProt ID (human)	RARG_HUMAN
UniProt ID (mouse)	RARG_MOUSE
UniProt AC (human)	P13631 (TFClass)
UniProt AC (mouse)	P18911 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 0 mouse
HT-SELEX	8
Methyl-HT-SELEX	2

PCM	RARG.H12RSNP.1.PSM.A.pcm
PWM	RARG.H12RSNP.1.PSM.A.pwm
PFM	RARG.H12RSNP.1.PSM.A.pfm
Alignment	RARG.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	RARG.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	RARG.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	RARG.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	RARG.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	RARG.H12RSNP.1.PSM.A_homer_format_0.001.txt RARG.H12RSNP.1.PSM.A_homer_format_0.0005.txt RARG.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	92.25	76.25	104.25	73.25
02	137.75	52.75	68.75	86.75
03	174.0	30.0	118.0	24.0
04	327.0	0.0	19.0	0.0
05	0.0	0.0	346.0	0.0
06	0.0	0.0	345.0	1.0
07	0.0	0.0	0.0	346.0
08	0.0	346.0	0.0	0.0
09	346.0	0.0	0.0	0.0
10	76.0	101.0	35.0	134.0
11	61.5	65.5	163.5	55.5
12	114.25	82.25	82.25	67.25

PFM

	A	C	G	T
01	0.267	0.22	0.301	0.212
02	0.398	0.152	0.199	0.251
03	0.503	0.087	0.341	0.069
04	0.945	0.0	0.055	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.997	0.003
07	0.0	0.0	0.0	1.0
08	0.0	1.0	0.0	0.0
09	1.0	0.0	0.0	0.0
10	0.22	0.292	0.101	0.387
11	0.178	0.189	0.473	0.16
12	0.33	0.238	0.238	0.194

PWM

	A	C	G	T
01	0.063	-0.124	0.184	-0.163
02	0.459	-0.484	-0.225	0.003
03	0.691	-1.028	0.306	-1.24
04	1.318	-4.097	-1.458	-4.097
05	-4.097	-4.097	1.374	-4.097
06	-4.097	-4.097	1.371	-3.576
07	-4.097	-4.097	-4.097	1.374
08	-4.097	1.374	-4.097	-4.097
09	1.374	-4.097	-4.097	-4.097
10	-0.127	0.153	-0.881	0.432
11	-0.334	-0.273	0.629	-0.435
12	0.274	-0.05	-0.05	-0.247

Standard thresholds

P-value	Threshold
0.001	3.47034
0.0005	4.31724
0.0001	7.87195