NR1I3.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I3.H12RSNP.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	11
Consensus	nddAGTTCRhn
GC content	42.75%
Information content (bits; total / per base)	11.088 / 1.008
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9974

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)	0.679	0.714	0.562	0.604	0.619	0.664	1.591	1.776	72.277	94.432

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.95	0.929	0.833	0.824	0.699	0.713
Overall, 2 experiments	best	0.962	0.936	0.907	0.882	0.766	0.767
Methyl HT-SELEX, 1 experiments	median	0.939	0.921	0.759	0.766	0.632	0.659
Methyl HT-SELEX, 1 experiments	best	0.939	0.921	0.759	0.766	0.632	0.659
Non-Methyl HT-SELEX, 1 experiments	median	0.962	0.936	0.907	0.882	0.766	0.767
Non-Methyl HT-SELEX, 1 experiments	best	0.962	0.936	0.907	0.882	0.766	0.767

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.552	0.113	0.342	0.333

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.H12RSNP.1.PSM.A.pcm
PWM	NR1I3.H12RSNP.1.PSM.A.pwm
PFM	NR1I3.H12RSNP.1.PSM.A.pfm
Alignment	NR1I3.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	NR1I3.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	NR1I3.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	NR1I3.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	NR1I3.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	NR1I3.H12RSNP.1.PSM.A_homer_format_0.001.txt NR1I3.H12RSNP.1.PSM.A_homer_format_0.0005.txt NR1I3.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2016.75	2749.75	2613.75	2593.75
02	5402.75	981.75	1574.75	2014.75
03	4532.0	554.0	2509.0	2379.0
04	9388.0	158.0	324.0	104.0
05	14.0	16.0	9943.0	1.0
06	1.0	0.0	4.0	9969.0
07	2.0	1.0	19.0	9952.0
08	12.0	9883.0	17.0	62.0
09	3113.0	260.0	6503.0	98.0
10	1528.75	2882.75	1338.75	4223.75
11	1803.5	2347.5	2226.5	3596.5

PFM

	A	C	G	T
01	0.202	0.276	0.262	0.26
02	0.542	0.098	0.158	0.202
03	0.454	0.056	0.252	0.239
04	0.941	0.016	0.032	0.01
05	0.001	0.002	0.997	0.0
06	0.0	0.0	0.0	0.999
07	0.0	0.0	0.002	0.998
08	0.001	0.991	0.002	0.006
09	0.312	0.026	0.652	0.01
10	0.153	0.289	0.134	0.423
11	0.181	0.235	0.223	0.361

PWM

	A	C	G	T
01	-0.212	0.098	0.047	0.039
02	0.773	-0.931	-0.459	-0.213
03	0.597	-1.501	0.006	-0.047
04	1.325	-2.745	-2.035	-3.156
05	-5.031	-4.915	1.382	-6.628
06	-6.628	-6.989	-5.982	1.385
07	-6.363	-6.628	-4.764	1.383
08	-5.162	1.376	-4.862	-3.659
09	0.222	-2.253	0.958	-3.214
10	-0.489	0.145	-0.621	0.527
11	-0.324	-0.06	-0.113	0.366

Standard thresholds

P-value	Threshold
0.001	3.93322
0.0005	5.33561
0.0001	7.84623