NR1I3.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I3.H12INVITRO.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	17
Consensus	nnWWAGTTCAYbnvvnh
GC content	38.48%
Information content (bits; total / per base)	14.821 / 0.872
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	395

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)	0.677	0.7	0.557	0.584	0.659	0.691	1.729	1.874	77.877	96.638

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.941	0.919	0.83	0.821	0.695	0.711
Overall, 2 experiments	best	0.978	0.966	0.921	0.905	0.77	0.779
Methyl HT-SELEX, 1 experiments	median	0.904	0.873	0.739	0.738	0.619	0.642
Methyl HT-SELEX, 1 experiments	best	0.904	0.873	0.739	0.738	0.619	0.642
Non-Methyl HT-SELEX, 1 experiments	median	0.978	0.966	0.921	0.905	0.77	0.779
Non-Methyl HT-SELEX, 1 experiments	best	0.978	0.966	0.921	0.905	0.77	0.779

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.581	0.11	0.223	0.294

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.1.PSM.A.pcm
PWM	NR1I3.H12INVITRO.1.PSM.A.pwm
PFM	NR1I3.H12INVITRO.1.PSM.A.pfm
Alignment	NR1I3.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	NR1I3.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	NR1I3.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	NR1I3.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	NR1I3.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	NR1I3.H12INVITRO.1.PSM.A_homer_format_0.001.txt NR1I3.H12INVITRO.1.PSM.A_homer_format_0.0005.txt NR1I3.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	74.0	116.0	104.0	101.0
02	60.75	134.75	125.75	73.75
03	264.0	19.0	41.0	71.0
04	285.0	6.0	51.0	53.0
05	394.0	0.0	1.0	0.0
06	0.0	0.0	395.0	0.0
07	0.0	0.0	0.0	395.0
08	0.0	0.0	0.0	395.0
09	0.0	395.0	0.0	0.0
10	392.0	0.0	3.0	0.0
11	24.0	72.0	14.0	285.0
12	58.0	88.0	154.0	95.0
13	108.0	118.0	106.0	63.0
14	200.0	53.0	92.0	50.0
15	159.0	111.0	64.0	61.0
16	119.75	80.75	87.75	106.75
17	76.5	77.5	74.5	166.5

PFM

	A	C	G	T
01	0.187	0.294	0.263	0.256
02	0.154	0.341	0.318	0.187
03	0.668	0.048	0.104	0.18
04	0.722	0.015	0.129	0.134
05	0.997	0.0	0.003	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.0	1.0	0.0	0.0
10	0.992	0.0	0.008	0.0
11	0.061	0.182	0.035	0.722
12	0.147	0.223	0.39	0.241
13	0.273	0.299	0.268	0.159
14	0.506	0.134	0.233	0.127
15	0.403	0.281	0.162	0.154
16	0.303	0.204	0.222	0.27
17	0.194	0.196	0.189	0.422

PWM

	A	C	G	T
01	-0.284	0.159	0.051	0.022
02	-0.477	0.307	0.238	-0.287
03	0.974	-1.587	-0.858	-0.324
04	1.05	-2.593	-0.647	-0.61
05	1.373	-4.206	-3.693	-4.206
06	-4.206	-4.206	1.375	-4.206
07	-4.206	-4.206	-4.206	1.375
08	-4.206	-4.206	-4.206	1.375
09	-4.206	1.375	-4.206	-4.206
10	1.367	-4.206	-3.105	-4.206
11	-1.369	-0.31	-1.867	1.05
12	-0.522	-0.113	0.439	-0.038
13	0.088	0.176	0.07	-0.441
14	0.698	-0.61	-0.07	-0.666
15	0.471	0.115	-0.426	-0.473
16	0.19	-0.198	-0.116	0.077
17	-0.251	-0.238	-0.277	0.516

Standard thresholds

P-value	Threshold
0.001	2.60871
0.0005	3.83541
0.0001	6.67681