VDR.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VDR.H12INVITRO.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	17
Consensus	nGRGTTCAYbSRGTKYR
GC content	49.37%
Information content (bits; total / per base)	16.16 / 0.951
Data sources	ChIP-Seq + HT-SELEX
Aligned words	726

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)	0.749	0.935	0.657	0.883	0.744	0.911	2.485	3.967	98.222	619.77
Mouse	10 (52)	0.753	0.87	0.674	0.782	0.713	0.835	2.448	2.967	124.745	227.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.75	0.752	0.633	0.644	0.566	0.585
Non-Methyl HT-SELEX, 4 experiments	best	0.999	0.999	0.977	0.976	0.808	0.832

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.H12INVITRO.0.PS.A.pcm
PWM	VDR.H12INVITRO.0.PS.A.pwm
PFM	VDR.H12INVITRO.0.PS.A.pfm
Alignment	VDR.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	VDR.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	VDR.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	VDR.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	VDR.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	VDR.H12INVITRO.0.PS.A_homer_format_0.001.txt VDR.H12INVITRO.0.PS.A_homer_format_0.0005.txt VDR.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	122.5	159.5	176.5	267.5
02	82.75	40.75	583.75	18.75
03	402.0	4.0	313.0	7.0
04	4.0	0.0	720.0	2.0
05	0.0	2.0	33.0	691.0
06	11.0	6.0	26.0	683.0
07	2.0	706.0	2.0	16.0
08	565.0	14.0	138.0	9.0
09	64.0	106.0	78.0	478.0
10	121.0	136.0	155.0	314.0
11	94.0	99.0	475.0	58.0
12	321.0	28.0	355.0	22.0
13	34.0	16.0	655.0	21.0
14	19.0	15.0	134.0	558.0
15	82.0	25.0	100.0	519.0
16	44.5	509.5	52.5	119.5
17	432.25	78.25	151.25	64.25

PFM

	A	C	G	T
01	0.169	0.22	0.243	0.368
02	0.114	0.056	0.804	0.026
03	0.554	0.006	0.431	0.01
04	0.006	0.0	0.992	0.003
05	0.0	0.003	0.045	0.952
06	0.015	0.008	0.036	0.941
07	0.003	0.972	0.003	0.022
08	0.778	0.019	0.19	0.012
09	0.088	0.146	0.107	0.658
10	0.167	0.187	0.213	0.433
11	0.129	0.136	0.654	0.08
12	0.442	0.039	0.489	0.03
13	0.047	0.022	0.902	0.029
14	0.026	0.021	0.185	0.769
15	0.113	0.034	0.138	0.715
16	0.061	0.702	0.072	0.165
17	0.595	0.108	0.208	0.088

PWM

	A	C	G	T
01	-0.389	-0.128	-0.028	0.385
02	-0.775	-1.463	1.162	-2.195
03	0.79	-3.479	0.541	-3.053
04	-3.479	-4.711	1.371	-3.916
05	-4.711	-3.916	-1.665	1.33
06	-2.673	-3.176	-1.891	1.319
07	-3.916	1.352	-3.916	-2.34
08	1.129	-2.46	-0.271	-2.845
09	-1.026	-0.531	-0.833	0.963
10	-0.401	-0.286	-0.156	0.544
11	-0.65	-0.599	0.956	-1.122
12	0.566	-1.821	0.666	-2.047
13	-1.637	-2.34	1.277	-2.09
14	-2.183	-2.398	-0.3	1.117
15	-0.784	-1.928	-0.589	1.045
16	-1.378	1.026	-1.219	-0.413
17	0.863	-0.83	-0.181	-1.022

Standard thresholds

P-value	Threshold
0.001	2.60521
0.0005	3.80561
0.0001	6.31356