NR1I3.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I3.H12INVITRO.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	vdRdbvdnbWRAGKKCA
GC content	50.31%
Information content (bits; total / per base)	10.66 / 0.627
Data sources	ChIP-Seq
Aligned words	976

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)	0.803	0.827	0.677	0.71	0.813	0.828	2.735	2.886	124.6	133.268

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.806	0.766	0.712	0.686	0.627	0.623
Overall, 2 experiments	best	0.883	0.843	0.786	0.753	0.684	0.673
Methyl HT-SELEX, 1 experiments	median	0.73	0.69	0.637	0.62	0.571	0.574
Methyl HT-SELEX, 1 experiments	best	0.73	0.69	0.637	0.62	0.571	0.574
Non-Methyl HT-SELEX, 1 experiments	median	0.883	0.843	0.786	0.753	0.684	0.673
Non-Methyl HT-SELEX, 1 experiments	best	0.883	0.843	0.786	0.753	0.684	0.673

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.543	0.021	0.227	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.H12INVITRO.0.P.B.pcm
PWM	NR1I3.H12INVITRO.0.P.B.pwm
PFM	NR1I3.H12INVITRO.0.P.B.pfm
Alignment	NR1I3.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	NR1I3.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	NR1I3.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	NR1I3.H12INVITRO.0.P.B_meme_format.meme
Transfac format	NR1I3.H12INVITRO.0.P.B_transfac_format.txt
Homer format	NR1I3.H12INVITRO.0.P.B_homer_format_0.001.txt NR1I3.H12INVITRO.0.P.B_homer_format_0.0005.txt NR1I3.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	388.0	165.0	333.0	90.0
02	412.0	77.0	349.0	138.0
03	155.0	49.0	634.0	138.0
04	101.0	91.0	483.0	301.0
05	123.0	241.0	204.0	408.0
06	137.0	488.0	233.0	118.0
07	463.0	100.0	194.0	219.0
08	298.0	191.0	284.0	203.0
09	120.0	575.0	146.0	135.0
10	613.0	76.0	80.0	207.0
11	295.0	101.0	572.0	8.0
12	792.0	1.0	91.0	92.0
13	4.0	2.0	962.0	8.0
14	9.0	16.0	375.0	576.0
15	92.0	99.0	185.0	600.0
16	4.0	885.0	23.0	64.0
17	895.0	21.0	22.0	38.0

PFM

	A	C	G	T
01	0.398	0.169	0.341	0.092
02	0.422	0.079	0.358	0.141
03	0.159	0.05	0.65	0.141
04	0.103	0.093	0.495	0.308
05	0.126	0.247	0.209	0.418
06	0.14	0.5	0.239	0.121
07	0.474	0.102	0.199	0.224
08	0.305	0.196	0.291	0.208
09	0.123	0.589	0.15	0.138
10	0.628	0.078	0.082	0.212
11	0.302	0.103	0.586	0.008
12	0.811	0.001	0.093	0.094
13	0.004	0.002	0.986	0.008
14	0.009	0.016	0.384	0.59
15	0.094	0.101	0.19	0.615
16	0.004	0.907	0.024	0.066
17	0.917	0.022	0.023	0.039

PWM

	A	C	G	T
01	0.461	-0.388	0.309	-0.985
02	0.521	-1.138	0.356	-0.565
03	-0.45	-1.578	0.951	-0.565
04	-0.872	-0.975	0.679	0.209
05	-0.678	-0.012	-0.178	0.511
06	-0.572	0.69	-0.046	-0.719
07	0.637	-0.882	-0.228	-0.107
08	0.199	-0.243	0.151	-0.183
09	-0.702	0.853	-0.509	-0.586
10	0.917	-1.151	-1.101	-0.163
11	0.189	-0.872	0.848	-3.23
12	1.173	-4.503	-0.975	-0.964
13	-3.76	-4.19	1.367	-3.23
14	-3.132	-2.629	0.427	0.855
15	-0.964	-0.892	-0.275	0.896
16	-3.76	1.283	-2.297	-1.319
17	1.295	-2.381	-2.338	-1.822

Standard thresholds

P-value	Threshold
0.001	4.61286
0.0005	5.48001
0.0001	7.23581