RARA.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARA.H12INVITRO.0.PSM.A
Gene (human)	RARA (GeneCards)
Gene synonyms (human)	NR1B1
Gene (mouse)	Rara
Gene synonyms (mouse)	Nr1b1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	nRAGGTCAhRn
GC content	52.82%
Information content (bits; total / per base)	11.821 / 1.075
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9748

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
Overall, 4 experiments	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
Methyl HT-SELEX, 1 experiments	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
Non-Methyl HT-SELEX, 3 experiments	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 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: 2.1.2.1.1
HGNC	HGNC:9864
MGI	MGI: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	RARA.H12INVITRO.0.PSM.A.pcm
PWM	RARA.H12INVITRO.0.PSM.A.pwm
PFM	RARA.H12INVITRO.0.PSM.A.pfm
Alignment	RARA.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	RARA.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	RARA.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	RARA.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	RARA.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	RARA.H12INVITRO.0.PSM.A_homer_format_0.001.txt RARA.H12INVITRO.0.PSM.A_homer_format_0.0005.txt RARA.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2765.25	1969.25	2206.25	2807.25
02	4890.75	458.75	3507.75	890.75
03	8663.0	14.0	1067.0	4.0
04	0.0	0.0	9748.0	0.0
05	0.0	0.0	9719.0	29.0
06	0.0	0.0	23.0	9725.0
07	0.0	9706.0	5.0	37.0
08	8296.0	0.0	1452.0	0.0
09	2346.0	3208.0	1148.0	3046.0
10	1476.5	1156.5	6020.5	1094.5
11	2616.25	1799.25	3430.25	1902.25

PFM

	A	C	G	T
01	0.284	0.202	0.226	0.288
02	0.502	0.047	0.36	0.091
03	0.889	0.001	0.109	0.0
04	0.0	0.0	1.0	0.0
05	0.0	0.0	0.997	0.003
06	0.0	0.0	0.002	0.998
07	0.0	0.996	0.001	0.004
08	0.851	0.0	0.149	0.0
09	0.241	0.329	0.118	0.312
10	0.151	0.119	0.618	0.112
11	0.268	0.185	0.352	0.195

PWM

	A	C	G	T
01	0.126	-0.213	-0.099	0.141
02	0.696	-1.666	0.364	-1.005
03	1.268	-5.009	-0.825	-5.96
04	-6.968	-6.968	1.386	-6.968
05	-6.968	-6.968	1.383	-4.356
06	-6.968	-6.968	-4.569	1.383
07	-6.968	1.381	-5.812	-4.128
08	1.224	-6.968	-0.517	-6.968
09	-0.038	0.275	-0.752	0.223
10	-0.5	-0.744	0.904	-0.799
11	0.071	-0.303	0.342	-0.247

Standard thresholds

P-value	Threshold
0.001	2.89016
0.0005	5.301275
0.0001	7.7877