RARA.H13RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARA.H13RSNP.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	10
Consensus	vAGGTCAvvR
GC content	54.37%
Information content (bits; total / per base)	10.01 / 1.001
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000
Previous names	RARA.H12RSNP.0.PSM.A

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)	0.73	0.812	0.549	0.662	0.709	0.824	1.89	2.58	58.77	144.721
Mouse	10 (46)	0.829	0.923	0.738	0.864	0.818	0.913	2.858	3.65	108.757	448.292

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.794	0.775	0.761	0.75	0.735	0.724
Overall, 4 experiments	best	0.98	0.965	0.976	0.958	0.956	0.935
Methyl HT-SELEX, 1 experiments	median	0.98	0.965	0.976	0.958	0.956	0.935
Methyl HT-SELEX, 1 experiments	best	0.98	0.965	0.976	0.958	0.956	0.935
Non-Methyl HT-SELEX, 3 experiments	median	0.611	0.589	0.554	0.55	0.527	0.528
Non-Methyl HT-SELEX, 3 experiments	best	0.978	0.962	0.969	0.949	0.943	0.919

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.617	5.938	0.166	0.109

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.581	0.056	0.579	0.273

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	RARA.H13RSNP.0.PSM.A.pcm
PWM	RARA.H13RSNP.0.PSM.A.pwm
PFM	RARA.H13RSNP.0.PSM.A.pfm
Threshold to P-value map	RARA.H13RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	RARA.H13RSNP.0.PSM.A_jaspar_format.txt
MEME format	RARA.H13RSNP.0.PSM.A_meme_format.meme
Transfac format	RARA.H13RSNP.0.PSM.A_transfac_format.txt
Homer format	RARA.H13RSNP.0.PSM.A_homer_format_0.001.txt RARA.H13RSNP.0.PSM.A_homer_format_0.0005.txt RARA.H13RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	452.0	98.0	399.0	51.0
02	694.0	6.0	288.0	12.0
03	19.0	0.0	973.0	8.0
04	23.0	9.0	734.0	234.0
05	21.0	106.0	71.0	802.0
06	8.0	960.0	22.0	10.0
07	982.0	9.0	6.0	3.0
08	504.0	93.0	320.0	83.0
09	272.0	92.0	551.0	85.0
10	184.0	70.0	630.0	116.0

PFM

	A	C	G	T
01	0.452	0.098	0.399	0.051
02	0.694	0.006	0.288	0.012
03	0.019	0.0	0.973	0.008
04	0.023	0.009	0.734	0.234
05	0.021	0.106	0.071	0.802
06	0.008	0.96	0.022	0.01
07	0.982	0.009	0.006	0.003
08	0.504	0.093	0.32	0.083
09	0.272	0.092	0.551	0.085
10	0.184	0.07	0.63	0.116

PWM

	A	C	G	T
01	0.589	-0.926	0.465	-1.563
02	1.017	-3.484	0.141	-2.909
03	-2.497	-4.982	1.354	-3.253
04	-2.32	-3.156	1.073	-0.066
05	-2.405	-0.849	-1.242	1.161
06	-3.253	1.34	-2.362	-3.066
07	1.363	-3.156	-3.484	-3.975
08	0.698	-0.977	0.245	-1.089
09	0.084	-0.988	0.787	-1.066
10	-0.304	-1.255	0.92	-0.76

Standard thresholds

P-value	Threshold
0.001	4.764665
0.0005	5.68438
0.0001	7.435775