MotifRARA.H12INVIVO.1.P.B
Gene (human)RARA
(GeneCards)
Gene synonyms (human)NR1B1
Gene (mouse)Rara
Gene synonyms (mouse)Nr1b1
LOGO
LOGO (reverse complement)
Motif subtype1
Quality
B
Motif length19
ConsensusvRRGKTCAnnnnvRGKdYW
GC content54.27%
Information content (bits; total / per base)11.67 / 0.614
Data sourcesChIP-Seq
Aligned words977

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) 0.749 0.852 0.609 0.796 0.731 0.836 2.402 3.827 50.208 129.721
Mouse 10 (46) 0.772 0.838 0.686 0.788 0.736 0.812 2.83 3.818 85.502 167.921

HT-SELEX benchmarking auROC10 auPRC10 auROC25 auPRC25 auROC50 auPRC50
Overall, 4 experiments median 0.77 0.756 0.728 0.713 0.68 0.667
best 0.978 0.969 0.943 0.924 0.877 0.854
Methyl HT-SELEX, 1 experiments median 0.978 0.969 0.943 0.924 0.877 0.854
best 0.978 0.969 0.943 0.924 0.877 0.854
Non-Methyl HT-SELEX, 3 experiments median 0.572 0.559 0.54 0.535 0.524 0.522
best 0.967 0.953 0.916 0.892 0.835 0.812

rSNP benchmarking, ADASTRA odds-ratio -log-Fisher's P Pearson r Kendall tau
# 1.875 2.898 0.156 0.078

rSNP benchmarking, SNP-SELEX auROC auPRC Pearson r Kendall tau
batch 2 0.523 0.057 0.486 0.228
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
01424.0186.0195.0172.0
02334.0107.0503.033.0
03521.04.0444.08.0
0435.010.0907.025.0
0530.018.0682.0247.0
0622.029.086.0840.0
0718.0791.0106.062.0
08849.058.058.012.0
09239.0239.0298.0201.0
10273.0243.0304.0157.0
11164.0271.0306.0236.0
12353.0138.0263.0223.0
13251.0152.0478.096.0
14574.053.0274.076.0
1567.041.0807.062.0
1658.034.0663.0222.0
17146.0138.0245.0448.0
1883.0691.089.0114.0
19695.082.082.0118.0
PFM
ACGT
010.4340.190.20.176
020.3420.110.5150.034
030.5330.0040.4540.008
040.0360.010.9280.026
050.0310.0180.6980.253
060.0230.030.0880.86
070.0180.810.1080.063
080.8690.0590.0590.012
090.2450.2450.3050.206
100.2790.2490.3110.161
110.1680.2770.3130.242
120.3610.1410.2690.228
130.2570.1560.4890.098
140.5880.0540.280.078
150.0690.0420.8260.063
160.0590.0350.6790.227
170.1490.1410.2510.459
180.0850.7070.0910.117
190.7110.0840.0840.121
PWM
ACGT
010.549-0.27-0.223-0.348
020.311-0.8160.719-1.958
030.754-3.7610.594-3.231
04-1.902-3.0441.307-2.22
05-2.048-2.5241.0220.011
06-2.339-2.08-1.0311.23
07-2.5241.17-0.826-1.351
081.241-1.416-1.416-2.886
09-0.022-0.0220.198-0.193
100.111-0.0050.217-0.438
11-0.3950.1030.224-0.034
120.366-0.5660.073-0.09
130.027-0.470.668-0.923
140.85-1.5030.114-1.152
15-1.275-1.7511.19-1.351
16-1.416-1.9290.994-0.095
17-0.51-0.5660.0030.603
18-1.0661.035-0.997-0.754
191.041-1.078-1.078-0.72
Standard thresholds
P-value Threshold
0.001 4.33431
0.0005 5.22441
0.0001 7.08946