MotifRARA.H12INVITRO.0.PSM.A
Gene (human)RARA
(GeneCards)
Gene synonyms (human)NR1B1
Gene (mouse)Rara
Gene synonyms (mouse)Nr1b1
LOGO
LOGO (reverse complement)
Motif subtype0
Quality
A
Motif length11
ConsensusnRAGGTCAhRn
GC content52.82%
Information content (bits; total / per base)11.821 / 1.075
Data sourcesChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words9748

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) 0.77 0.806 0.583 0.638 0.749 0.811 2.039 2.379 84.678 142.77
Mouse 10 (46) 0.812 0.899 0.693 0.79 0.787 0.87 2.358 2.794 101.403 379.398

HT-SELEX benchmarking auROC10 auPRC10 auROC25 auPRC25 auROC50 auPRC50
Overall, 4 experiments median 0.804 0.787 0.776 0.764 0.748 0.739
best 0.991 0.984 0.986 0.977 0.973 0.96
Methyl HT-SELEX, 1 experiments median 0.991 0.984 0.986 0.977 0.973 0.96
best 0.991 0.984 0.986 0.977 0.973 0.96
Non-Methyl HT-SELEX, 3 experiments median 0.62 0.594 0.571 0.559 0.541 0.538
best 0.988 0.979 0.98 0.969 0.956 0.94

rSNP benchmarking, ADASTRA odds-ratio -log-Fisher's P Pearson r Kendall tau
# 2.231 4.348 0.193 0.094

rSNP benchmarking, SNP-SELEX auROC auPRC Pearson r Kendall tau
batch 2 0.549 0.074 0.453 0.152
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
012765.251969.252206.252807.25
024890.75458.753507.75890.75
038663.014.01067.04.0
040.00.09748.00.0
050.00.09719.029.0
060.00.023.09725.0
070.09706.05.037.0
088296.00.01452.00.0
092346.03208.01148.03046.0
101476.51156.56020.51094.5
112616.251799.253430.251902.25
PFM
ACGT
010.2840.2020.2260.288
020.5020.0470.360.091
030.8890.0010.1090.0
040.00.01.00.0
050.00.00.9970.003
060.00.00.0020.998
070.00.9960.0010.004
080.8510.00.1490.0
090.2410.3290.1180.312
100.1510.1190.6180.112
110.2680.1850.3520.195
PWM
ACGT
010.126-0.213-0.0990.141
020.696-1.6660.364-1.005
031.268-5.009-0.825-5.96
04-6.968-6.9681.386-6.968
05-6.968-6.9681.383-4.356
06-6.968-6.968-4.5691.383
07-6.9681.381-5.812-4.128
081.224-6.968-0.517-6.968
09-0.0380.275-0.7520.223
10-0.5-0.7440.904-0.799
110.071-0.3030.342-0.247
Standard thresholds
P-value Threshold
0.001 2.89016
0.0005 5.301275
0.0001 7.7877