NR1I3.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I3.H12INVIVO.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	17
Consensus	vRRKbYWnvhRRGKbCA
GC content	51.29%
Information content (bits; total / per base)	11.138 / 0.655
Data sources	ChIP-Seq
Aligned words	977

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)	0.8	0.832	0.703	0.743	0.796	0.823	2.8	3.08	123.794	151.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.735	0.704	0.65	0.632	0.591	0.586
Overall, 2 experiments	best	0.796	0.759	0.703	0.676	0.629	0.618
Methyl HT-SELEX, 1 experiments	median	0.673	0.648	0.597	0.588	0.553	0.554
Methyl HT-SELEX, 1 experiments	best	0.673	0.648	0.597	0.588	0.553	0.554
Non-Methyl HT-SELEX, 1 experiments	median	0.796	0.759	0.703	0.676	0.629	0.618
Non-Methyl HT-SELEX, 1 experiments	best	0.796	0.759	0.703	0.676	0.629	0.618

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.59	0.026	-0.047	-0.098

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.0.P.B.pcm
PWM	NR1I3.H12INVIVO.0.P.B.pwm
PFM	NR1I3.H12INVIVO.0.P.B.pfm
Alignment	NR1I3.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	NR1I3.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	NR1I3.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	NR1I3.H12INVIVO.0.P.B_meme_format.meme
Transfac format	NR1I3.H12INVIVO.0.P.B_transfac_format.txt
Homer format	NR1I3.H12INVIVO.0.P.B_homer_format_0.001.txt NR1I3.H12INVIVO.0.P.B_homer_format_0.0005.txt NR1I3.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	352.0	169.0	363.0	93.0
02	524.0	20.0	375.0	58.0
03	122.0	15.0	758.0	82.0
04	74.0	21.0	560.0	322.0
05	51.0	211.0	204.0	511.0
06	122.0	607.0	119.0	129.0
07	666.0	70.0	92.0	149.0
08	241.0	208.0	372.0	156.0
09	166.0	470.0	184.0	157.0
10	484.0	119.0	113.0	261.0
11	269.0	129.0	553.0	26.0
12	736.0	5.0	144.0	92.0
13	8.0	0.0	954.0	15.0
14	26.0	20.0	359.0	572.0
15	80.0	144.0	210.0	543.0
16	24.0	841.0	33.0	79.0
17	860.0	38.0	38.0	41.0

PFM

	A	C	G	T
01	0.36	0.173	0.372	0.095
02	0.536	0.02	0.384	0.059
03	0.125	0.015	0.776	0.084
04	0.076	0.021	0.573	0.33
05	0.052	0.216	0.209	0.523
06	0.125	0.621	0.122	0.132
07	0.682	0.072	0.094	0.153
08	0.247	0.213	0.381	0.16
09	0.17	0.481	0.188	0.161
10	0.495	0.122	0.116	0.267
11	0.275	0.132	0.566	0.027
12	0.753	0.005	0.147	0.094
13	0.008	0.0	0.976	0.015
14	0.027	0.02	0.367	0.585
15	0.082	0.147	0.215	0.556
16	0.025	0.861	0.034	0.081
17	0.88	0.039	0.039	0.042

PWM

	A	C	G	T
01	0.363	-0.365	0.394	-0.954
02	0.76	-2.427	0.426	-1.416
03	-0.687	-2.689	1.128	-1.078
04	-1.178	-2.382	0.826	0.275
05	-1.54	-0.145	-0.179	0.735
06	-0.687	0.906	-0.712	-0.632
07	0.999	-1.232	-0.965	-0.49
08	-0.013	-0.159	0.418	-0.444
09	-0.383	0.651	-0.281	-0.438
10	0.68	-0.712	-0.763	0.066
11	0.096	-0.632	0.813	-2.183
12	1.098	-3.6	-0.524	-0.965
13	-3.231	-4.962	1.357	-2.689
14	-2.183	-2.427	0.383	0.847
15	-1.102	-0.524	-0.15	0.795
16	-2.258	1.231	-1.958	-1.114
17	1.254	-1.823	-1.823	-1.751

Standard thresholds

P-value	Threshold
0.001	4.47931
0.0005	5.35106
0.0001	7.15641