NR1I3.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I3.H12INVIVO.1.PSM.A
Gene (human)	NR1I3 (GeneCards)
Gene synonyms (human)	CAR
Gene (mouse)	Nr1i3
Gene synonyms (mouse)	Car
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	9
Consensus	hRAGKTCAb
GC content	49.21%
Information content (bits; total / per base)	9.553 / 1.061
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	953

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
Mouse	6 (6)	0.783	0.803	0.688	0.707	0.727	0.751	1.988	2.085	103.542	106.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.845	0.803	0.738	0.719	0.64	0.643
Overall, 2 experiments	best	0.934	0.889	0.842	0.811	0.714	0.711
Methyl HT-SELEX, 1 experiments	median	0.756	0.717	0.635	0.627	0.566	0.576
Methyl HT-SELEX, 1 experiments	best	0.756	0.717	0.635	0.627	0.566	0.576
Non-Methyl HT-SELEX, 1 experiments	median	0.934	0.889	0.842	0.811	0.714	0.711
Non-Methyl HT-SELEX, 1 experiments	best	0.934	0.889	0.842	0.811	0.714	0.711

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.622	0.03	-0.144	-0.216

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	VDR (NR1I) {2.1.2.4} (TFClass)
TFClass ID	TFClass: 2.1.2.4.3
HGNC	HGNC:7969
MGI	MGI:1346307
EntrezGene (human)	GeneID:9970 (SSTAR profile)
EntrezGene (mouse)	GeneID:12355 (SSTAR profile)
UniProt ID (human)	NR1I3_HUMAN
UniProt ID (mouse)	NR1I3_MOUSE
UniProt AC (human)	Q14994 (TFClass)
UniProt AC (mouse)	O35627 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 6 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	NR1I3.H12INVIVO.1.PSM.A.pcm
PWM	NR1I3.H12INVIVO.1.PSM.A.pwm
PFM	NR1I3.H12INVIVO.1.PSM.A.pfm
Alignment	NR1I3.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	NR1I3.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	NR1I3.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	NR1I3.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	NR1I3.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	NR1I3.H12INVIVO.1.PSM.A_homer_format_0.001.txt NR1I3.H12INVIVO.1.PSM.A_homer_format_0.0005.txt NR1I3.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	444.0	204.0	138.0	167.0
02	318.0	169.0	459.0	7.0
03	822.0	0.0	124.0	7.0
04	1.0	3.0	947.0	2.0
05	6.0	2.0	528.0	417.0
06	33.0	25.0	49.0	846.0
07	2.0	922.0	11.0	18.0
08	867.0	72.0	1.0	13.0
09	138.0	203.0	364.0	248.0

PFM

	A	C	G	T
01	0.466	0.214	0.145	0.175
02	0.334	0.177	0.482	0.007
03	0.863	0.0	0.13	0.007
04	0.001	0.003	0.994	0.002
05	0.006	0.002	0.554	0.438
06	0.035	0.026	0.051	0.888
07	0.002	0.967	0.012	0.019
08	0.91	0.076	0.001	0.014
09	0.145	0.213	0.382	0.26

PWM

	A	C	G	T
01	0.619	-0.154	-0.541	-0.352
02	0.287	-0.34	0.652	-3.315
03	1.233	-4.941	-0.646	-3.315
04	-4.482	-3.93	1.375	-4.168
05	-3.437	-4.168	0.792	0.557
06	-1.933	-2.195	-1.554	1.262
07	-4.168	1.348	-2.938	-2.499
08	1.287	-1.18	-4.482	-2.792
09	-0.541	-0.159	0.421	0.04

Standard thresholds

P-value	Threshold
0.001	4.80165
0.0005	5.77832
0.0001	7.62709