NR1I3.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I3.H12RSNP.0.P.B
Gene (human)	NR1I3 (GeneCards)
Gene synonyms (human)	CAR
Gene (mouse)	Nr1i3
Gene synonyms (mouse)	Car
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	19
Consensus	bhvRGKbSWnvdRRGKbCA
GC content	52.48%
Information content (bits; total / per base)	10.884 / 0.573
Data sources	ChIP-Seq
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)	0.792	0.824	0.659	0.7	0.808	0.831	2.918	3.095	130.497	147.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.719	0.688	0.638	0.62	0.583	0.578
Overall, 2 experiments	best	0.77	0.734	0.678	0.654	0.611	0.602
Methyl HT-SELEX, 1 experiments	median	0.668	0.641	0.598	0.586	0.555	0.554
Methyl HT-SELEX, 1 experiments	best	0.668	0.641	0.598	0.586	0.555	0.554
Non-Methyl HT-SELEX, 1 experiments	median	0.77	0.734	0.678	0.654	0.611	0.602
Non-Methyl HT-SELEX, 1 experiments	best	0.77	0.734	0.678	0.654	0.611	0.602

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.656	0.027	-0.144	-0.072

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.0.P.B.pcm
PWM	NR1I3.H12RSNP.0.P.B.pwm
PFM	NR1I3.H12RSNP.0.P.B.pfm
Alignment	NR1I3.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	NR1I3.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	NR1I3.H12RSNP.0.P.B_jaspar_format.txt
MEME format	NR1I3.H12RSNP.0.P.B_meme_format.meme
Transfac format	NR1I3.H12RSNP.0.P.B_transfac_format.txt
Homer format	NR1I3.H12RSNP.0.P.B_homer_format_0.001.txt NR1I3.H12RSNP.0.P.B_homer_format_0.0005.txt NR1I3.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	163.0	408.0	197.0	185.0
02	340.0	282.0	123.0	208.0
03	401.0	163.0	343.0	46.0
04	479.0	46.0	360.0	68.0
05	123.0	7.0	755.0	68.0
06	68.0	21.0	579.0	285.0
07	53.0	256.0	208.0	436.0
08	121.0	583.0	139.0	110.0
09	571.0	79.0	116.0	187.0
10	298.0	171.0	319.0	165.0
11	140.0	488.0	197.0	128.0
12	494.0	126.0	136.0	197.0
13	239.0	120.0	565.0	29.0
14	683.0	2.0	146.0	122.0
15	9.0	1.0	940.0	3.0
16	19.0	11.0	367.0	556.0
17	107.0	115.0	208.0	523.0
18	9.0	773.0	59.0	112.0
19	789.0	41.0	53.0	70.0

PFM

	A	C	G	T
01	0.171	0.428	0.207	0.194
02	0.357	0.296	0.129	0.218
03	0.421	0.171	0.36	0.048
04	0.503	0.048	0.378	0.071
05	0.129	0.007	0.792	0.071
06	0.071	0.022	0.608	0.299
07	0.056	0.269	0.218	0.458
08	0.127	0.612	0.146	0.115
09	0.599	0.083	0.122	0.196
10	0.313	0.179	0.335	0.173
11	0.147	0.512	0.207	0.134
12	0.518	0.132	0.143	0.207
13	0.251	0.126	0.593	0.03
14	0.717	0.002	0.153	0.128
15	0.009	0.001	0.986	0.003
16	0.02	0.012	0.385	0.583
17	0.112	0.121	0.218	0.549
18	0.009	0.811	0.062	0.118
19	0.828	0.043	0.056	0.073

PWM

	A	C	G	T
01	-0.376	0.535	-0.189	-0.251
02	0.353	0.167	-0.654	-0.135
03	0.518	-0.376	0.362	-1.615
04	0.695	-1.615	0.41	-1.236
05	-0.654	-3.315	1.148	-1.236
06	-1.236	-2.357	0.884	0.178
07	-1.478	0.071	-0.135	0.601
08	-0.671	0.891	-0.534	-0.765
09	0.87	-1.09	-0.712	-0.24
10	0.222	-0.329	0.29	-0.364
11	-0.527	0.713	-0.189	-0.615
12	0.726	-0.631	-0.555	-0.189
13	0.003	-0.679	0.859	-2.056
14	1.049	-4.168	-0.485	-0.663
15	-3.109	-4.482	1.367	-3.93
16	-2.45	-2.938	0.43	0.843
17	-0.792	-0.721	-0.135	0.782
18	-3.109	1.172	-1.374	-0.747
19	1.192	-1.726	-1.478	-1.208

Standard thresholds

P-value	Threshold
0.001	4.56306
0.0005	5.41726
0.0001	7.17286