MotifRARA.H12INVIVO.3.P.B
Gene (human)RARA
(GeneCards)
Gene synonyms (human)NR1B1
Gene (mouse)Rara
Gene synonyms (mouse)Nr1b1
LOGO
LOGO (reverse complement)
Motif subtype3
Quality
B
Motif length21
ConsensusvdbvvdRAGKTCARRRhSRdb
GC content53.35%
Information content (bits; total / per base)14.146 / 0.674
Data sourcesChIP-Seq
Aligned words944

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 (29) 0.684 0.765 0.48 0.62 0.72 0.806 2.179 3.346 28.495 147.721
Mouse 10 (46) 0.817 0.911 0.744 0.884 0.833 0.918 5.173 8.001 112.956 473.456

HT-SELEX benchmarking auROC10 auPRC10 auROC25 auPRC25 auROC50 auPRC50
Overall, 4 experiments median 0.759 0.742 0.726 0.711 0.688 0.674
best 0.961 0.937 0.933 0.902 0.877 0.845
Methyl HT-SELEX, 1 experiments median 0.959 0.937 0.927 0.896 0.865 0.834
best 0.959 0.937 0.927 0.896 0.865 0.834
Non-Methyl HT-SELEX, 3 experiments median 0.558 0.547 0.526 0.526 0.51 0.514
best 0.961 0.937 0.933 0.902 0.877 0.845

rSNP benchmarking, ADASTRA odds-ratio -log-Fisher's P Pearson r Kendall tau
# 2.911 6.945 0.19 0.111

rSNP benchmarking, SNP-SELEX auROC auPRC Pearson r Kendall tau
batch 2 0.582 0.064 0.459 0.221
TF superclassZinc-coordinating DNA-binding domains {2} (TFClass)
TF classNuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF familyThyroid hormone receptor-related {2.1.2} (TFClass)
TF subfamilyRAR (NR1B) {2.1.2.1} (TFClass)
TFClass IDTFClass: 2.1.2.1.1
HGNCHGNC:9864
MGIMGI:97856
EntrezGene (human)GeneID:5914
(SSTAR profile)
EntrezGene (mouse)GeneID:19401
(SSTAR profile)
UniProt ID (human)RARA_HUMAN
UniProt ID (mouse)RARA_MOUSE
UniProt AC (human)P10276
(TFClass)
UniProt AC (mouse)P11416
(TFClass)
GRECO-DB-TF
yes
ChIP-Seq 5 human, 10 mouse
HT-SELEX 3
Methyl-HT-SELEX 1
PCM
ACGT
01152.0163.0551.078.0
02277.088.0440.0139.0
03110.0149.0202.0483.0
04125.0538.0165.0116.0
05494.0199.0156.095.0
06367.086.0363.0128.0
07380.042.0492.030.0
08723.04.0215.02.0
0945.09.0883.07.0
1010.06.0480.0448.0
1127.033.048.0836.0
1220.0863.049.012.0
13916.013.012.03.0
14615.076.0198.055.0
15167.077.0649.051.0
1687.085.0687.085.0
17173.0189.0134.0448.0
1895.0563.0189.097.0
19635.045.0153.0111.0
20117.0114.0500.0213.0
21103.0308.0361.0172.0
PFM
ACGT
010.1610.1730.5840.083
020.2930.0930.4660.147
030.1170.1580.2140.512
040.1320.570.1750.123
050.5230.2110.1650.101
060.3890.0910.3850.136
070.4030.0440.5210.032
080.7660.0040.2280.002
090.0480.010.9350.007
100.0110.0060.5080.475
110.0290.0350.0510.886
120.0210.9140.0520.013
130.970.0140.0130.003
140.6510.0810.210.058
150.1770.0820.6880.054
160.0920.090.7280.09
170.1830.20.1420.475
180.1010.5960.20.103
190.6730.0480.1620.118
200.1240.1210.530.226
210.1090.3260.3820.182
PWM
ACGT
01-0.436-0.3670.844-1.093
020.159-0.9740.62-0.524
03-0.755-0.456-0.1540.712
04-0.6290.82-0.355-0.703
050.735-0.169-0.41-0.899
060.439-0.9970.428-0.606
070.474-1.6930.731-2.014
081.115-3.728-0.092-4.159
09-1.627-3.11.314-3.306
10-3.01-3.4280.7060.638
11-2.114-1.924-1.5651.26
12-2.3931.291-1.545-2.853
131.351-2.782-2.853-3.921
140.953-1.118-0.174-1.433
15-0.343-1.1051.007-1.506
16-0.986-1.0081.064-1.008
17-0.308-0.22-0.5610.638
18-0.8990.865-0.22-0.879
190.985-1.627-0.429-0.746
20-0.694-0.720.747-0.102
21-0.820.2650.423-0.314
Standard thresholds
P-value Threshold
0.001 3.59561
0.0005 4.63096
0.0001 6.79571