VDR.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VDR.H12INVIVO.0.PS.A
Gene (human)	VDR (GeneCards)
Gene synonyms (human)	NR1I1
Gene (mouse)	Vdr
Gene synonyms (mouse)	Nr1i1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	16
Consensus	vRGKYSAnnRRGKKYv
GC content	57.66%
Information content (bits; total / per base)	11.661 / 0.729
Data sources	ChIP-Seq + HT-SELEX
Aligned words	918

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
Human	45 (197)	0.818	0.98	0.77	0.968	0.808	0.97	3.501	5.967	143.131	835.108
Mouse	10 (52)	0.824	0.915	0.765	0.858	0.797	0.908	3.309	4.029	158.293	273.509

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.747	0.744	0.628	0.638	0.563	0.581
Non-Methyl HT-SELEX, 4 experiments	best	0.998	0.998	0.972	0.97	0.802	0.826

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: 2.1.2.4.1
HGNC	HGNC:12679
MGI	MGI:103076
EntrezGene (human)	GeneID:7421 (SSTAR profile)
EntrezGene (mouse)	GeneID:22337 (SSTAR profile)
UniProt ID (human)	VDR_HUMAN
UniProt ID (mouse)	VDR_MOUSE
UniProt AC (human)	P11473 (TFClass)
UniProt AC (mouse)	P48281 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	45 human, 10 mouse
HT-SELEX	4
Methyl-HT-SELEX	0

PCM	VDR.H12INVIVO.0.PS.A.pcm
PWM	VDR.H12INVIVO.0.PS.A.pwm
PFM	VDR.H12INVIVO.0.PS.A.pfm
Alignment	VDR.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	VDR.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	VDR.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	VDR.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	VDR.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	VDR.H12INVIVO.0.PS.A_homer_format_0.001.txt VDR.H12INVIVO.0.PS.A_homer_format_0.0005.txt VDR.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	260.0	117.0	461.0	80.0
02	452.0	19.0	431.0	16.0
03	43.0	5.0	813.0	57.0
04	49.0	8.0	664.0	197.0
05	10.0	146.0	130.0	632.0
06	36.0	703.0	92.0	87.0
07	739.0	24.0	121.0	34.0
08	133.0	284.0	281.0	220.0
09	248.0	190.0	136.0	344.0
10	122.0	100.0	662.0	34.0
11	375.0	33.0	501.0	9.0
12	44.0	6.0	859.0	9.0
13	23.0	29.0	344.0	522.0
14	40.0	125.0	151.0	602.0
15	15.0	654.0	60.0	189.0
16	513.0	151.0	169.0	85.0

PFM

	A	C	G	T
01	0.283	0.127	0.502	0.087
02	0.492	0.021	0.469	0.017
03	0.047	0.005	0.886	0.062
04	0.053	0.009	0.723	0.215
05	0.011	0.159	0.142	0.688
06	0.039	0.766	0.1	0.095
07	0.805	0.026	0.132	0.037
08	0.145	0.309	0.306	0.24
09	0.27	0.207	0.148	0.375
10	0.133	0.109	0.721	0.037
11	0.408	0.036	0.546	0.01
12	0.048	0.007	0.936	0.01
13	0.025	0.032	0.375	0.569
14	0.044	0.136	0.164	0.656
15	0.016	0.712	0.065	0.206
16	0.559	0.164	0.184	0.093

PWM

	A	C	G	T
01	0.124	-0.667	0.694	-1.04
02	0.674	-2.413	0.627	-2.569
03	-1.643	-3.54	1.26	-1.371
04	-1.517	-3.171	1.058	-0.151
05	-2.983	-0.448	-0.563	1.008
06	-1.813	1.114	-0.903	-0.958
07	1.164	-2.197	-0.634	-1.868
08	-0.54	0.212	0.201	-0.042
09	0.077	-0.187	-0.518	0.402
10	-0.625	-0.821	1.055	-1.868
11	0.488	-1.896	0.777	-3.073
12	-1.621	-3.401	1.314	-3.073
13	-2.236	-2.019	0.402	0.818
14	-1.713	-0.601	-0.415	0.96
15	-2.628	1.042	-1.321	-0.193
16	0.8	-0.415	-0.303	-0.981

Standard thresholds

P-value	Threshold
0.001	4.34171
0.0005	5.24486
0.0001	7.12451