VDR.H12INVITRO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VDR.H12INVITRO.1.PS.A
Gene (human)	VDR (GeneCards)
Gene synonyms (human)	NR1I1
Gene (mouse)	Vdr
Gene synonyms (mouse)	Nr1i1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	8
Consensus	GGGTTCAb
GC content	52.64%
Information content (bits; total / per base)	10.166 / 1.271
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000

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)	0.699	0.9	0.549	0.826	0.67	0.87	1.645	2.906	62.143	446.187
Mouse	10 (52)	0.711	0.822	0.574	0.697	0.666	0.774	1.647	2.021	79.033	138.569

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.743	0.719	0.641	0.635	0.575	0.583
Non-Methyl HT-SELEX, 4 experiments	best	0.984	0.976	0.946	0.932	0.808	0.814

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

PCM

	A	C	G	T
01	228.0	15.0	745.0	12.0
02	321.0	0.0	676.0	3.0
03	5.0	0.0	994.0	1.0
04	2.0	5.0	290.0	703.0
05	7.0	22.0	49.0	922.0
06	8.0	957.0	8.0	27.0
07	970.0	12.0	9.0	9.0
08	155.0	225.0	204.0	416.0

PFM

	A	C	G	T
01	0.228	0.015	0.745	0.012
02	0.321	0.0	0.676	0.003
03	0.005	0.0	0.994	0.001
04	0.002	0.005	0.29	0.703
05	0.007	0.022	0.049	0.922
06	0.008	0.957	0.008	0.027
07	0.97	0.012	0.009	0.009
08	0.155	0.225	0.204	0.416

PWM

	A	C	G	T
01	-0.091	-2.711	1.087	-2.909
02	0.248	-4.982	0.99	-3.975
03	-3.622	-4.982	1.375	-4.525
04	-4.213	-3.622	0.147	1.029
05	-3.362	-2.362	-1.602	1.3
06	-3.253	1.337	-3.253	-2.171
07	1.351	-2.909	-3.156	-3.156
08	-0.474	-0.105	-0.202	0.506

Standard thresholds

P-value	Threshold
0.001	4.36317
0.0005	5.465555
0.0001	7.72998