NR1I3.H12INVITRO.2.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1I3.H12INVITRO.2.M.C
Gene (human)	NR1I3 (GeneCards)
Gene synonyms (human)	CAR
Gene (mouse)	Nr1i3
Gene synonyms (mouse)	Car
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	19
Consensus	nbWWAGTTCGYnnRRvbYh
GC content	40.75%
Information content (bits; total / per base)	15.848 / 0.834
Data sources	Methyl-HT-SELEX
Aligned words	1579

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)	0.666	0.682	0.553	0.574	0.63	0.668	1.648	1.776	59.708	82.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.953	0.943	0.824	0.824	0.686	0.708
Overall, 2 experiments	best	0.97	0.957	0.907	0.889	0.756	0.765
Methyl HT-SELEX, 1 experiments	median	0.936	0.928	0.742	0.758	0.617	0.651
Methyl HT-SELEX, 1 experiments	best	0.936	0.928	0.742	0.758	0.617	0.651
Non-Methyl HT-SELEX, 1 experiments	median	0.97	0.957	0.907	0.889	0.756	0.765
Non-Methyl HT-SELEX, 1 experiments	best	0.97	0.957	0.907	0.889	0.756	0.765

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.502	0.089	0.191	0.255

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.2.M.C.pcm
PWM	NR1I3.H12INVITRO.2.M.C.pwm
PFM	NR1I3.H12INVITRO.2.M.C.pfm
Alignment	NR1I3.H12INVITRO.2.M.C.words.tsv
Threshold to P-value map	NR1I3.H12INVITRO.2.M.C.thr
Motif in other formats
JASPAR format	NR1I3.H12INVITRO.2.M.C_jaspar_format.txt
MEME format	NR1I3.H12INVITRO.2.M.C_meme_format.meme
Transfac format	NR1I3.H12INVITRO.2.M.C_transfac_format.txt
Homer format	NR1I3.H12INVITRO.2.M.C_homer_format_0.001.txt NR1I3.H12INVITRO.2.M.C_homer_format_0.0005.txt NR1I3.H12INVITRO.2.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	339.25	411.25	427.25	401.25
02	215.75	583.75	358.75	420.75
03	1135.0	96.0	148.0	200.0
04	983.0	5.0	223.0	368.0
05	1579.0	0.0	0.0	0.0
06	0.0	0.0	1579.0	0.0
07	0.0	0.0	0.0	1579.0
08	0.0	0.0	0.0	1579.0
09	0.0	1579.0	0.0	0.0
10	440.0	2.0	1137.0	0.0
11	117.0	596.0	81.0	785.0
12	261.0	362.0	459.0	497.0
13	395.0	351.0	564.0	269.0
14	928.0	60.0	390.0	201.0
15	1189.0	122.0	186.0	82.0
16	532.0	437.0	450.0	160.0
17	121.0	269.0	304.0	885.0
18	102.25	230.25	110.25	1136.25
19	245.5	537.5	165.5	630.5

PFM

	A	C	G	T
01	0.215	0.26	0.271	0.254
02	0.137	0.37	0.227	0.266
03	0.719	0.061	0.094	0.127
04	0.623	0.003	0.141	0.233
05	1.0	0.0	0.0	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	0.279	0.001	0.72	0.0
11	0.074	0.377	0.051	0.497
12	0.165	0.229	0.291	0.315
13	0.25	0.222	0.357	0.17
14	0.588	0.038	0.247	0.127
15	0.753	0.077	0.118	0.052
16	0.337	0.277	0.285	0.101
17	0.077	0.17	0.193	0.56
18	0.065	0.146	0.07	0.72
19	0.155	0.34	0.105	0.399

PWM

	A	C	G	T
01	-0.151	0.041	0.079	0.016
02	-0.6	0.39	-0.095	0.063
03	1.053	-1.4	-0.973	-0.675
04	0.91	-4.06	-0.568	-0.07
05	1.383	-5.373	-5.373	-5.373
06	-5.373	-5.373	1.383	-5.373
07	-5.373	-5.373	-5.373	1.383
08	-5.373	-5.373	-5.373	1.383
09	-5.373	1.383	-5.373	-5.373
10	0.108	-4.637	1.055	-5.373
11	-1.205	0.41	-1.566	0.685
12	-0.411	-0.086	0.15	0.229
13	0.001	-0.117	0.355	-0.381
14	0.852	-1.858	-0.012	-0.67
15	1.1	-1.164	-0.747	-1.554
16	0.297	0.101	0.13	-0.896
17	-1.172	-0.381	-0.26	0.805
18	-1.338	-0.536	-1.264	1.054
19	-0.472	0.307	-0.863	0.467

Standard thresholds

P-value	Threshold
0.001	1.15921
0.0005	2.68166
0.0001	6.19426