SLC2A4RG.H13RSNP.0.PSG.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SLC2A4RG.H13RSNP.0.PSG.D
Gene (human)	SLC2A4RG (GeneCards)
Gene synonyms (human)
Gene (mouse)
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	10
Consensus	nGCCGGCCGG
GC content	92.48%
Information content (bits; total / per base)	15.083 / 1.508
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX
Aligned words	310
Previous names

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	Centrality, median	Centrality, best
Overall	2 (4)	0.829	0.844	0.682	0.717	0.529	0.574	26.515	28.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 3 experiments	median	1.0	1.0	0.999	0.999	0.996	0.994
overall, 3 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999
Lysate, 1 experiments	median	1.0	1.0	0.999	0.999	0.88	0.915
Lysate, 1 experiments	best	1.0	1.0	0.999	0.999	0.88	0.915
IVT, 1 experiments	median	0.999	0.999	0.998	0.997	0.996	0.994
IVT, 1 experiments	best	0.999	0.999	0.998	0.997	0.996	0.994
GFPIVT, 1 experiments	median	1.0	1.0	1.0	1.0	1.0	0.999
GFPIVT, 1 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
overall, 3 experiments	median	202.046	0.91	0.965	0.949
overall, 3 experiments	best	470.569	0.94	0.977	0.968
Lysate, 1 experiments	median	241.62	0.936	0.975	0.961
Lysate, 1 experiments	best	470.569	0.94	0.977	0.968
IVT, 1 experiments	median	142.284	0.864	0.936	0.889
IVT, 1 experiments	best	142.284	0.864	0.936	0.889
GFPIVT, 1 experiments	median	202.046	0.91	0.965	0.949
GFPIVT, 1 experiments	best	209.959	0.914	0.969	0.956

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	Other with up to three adjacent zinc fingers {2.3.2} (TFClass)
TF subfamily	CR1-CR2 {2.3.2.255} (TFClass)
TFClass ID	TFClass: 2.3.2.255.1
HGNC
MGI
EntrezGene (human)
EntrezGene (mouse)
UniProt ID (human)	S2A4R_HUMAN
UniProt ID (mouse)
UniProt AC (human)	Q9NR83 (TFClass)
UniProt AC (mouse)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 0 mouse
HT-SELEX	3 overall: 1 Lysate, 1 IVT, 1 GFPIVT
Genomic HT-SELEX	3 overall: 1 Lysate, 1 IVT, 1 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	SLC2A4RG.H13RSNP.0.PSG.D.pcm
PWM	SLC2A4RG.H13RSNP.0.PSG.D.pwm
PFM	SLC2A4RG.H13RSNP.0.PSG.D.pfm
Threshold to P-value map	SLC2A4RG.H13RSNP.0.PSG.D.thr
Motif in other formats
JASPAR format	SLC2A4RG.H13RSNP.0.PSG.D_jaspar_format.txt
MEME format	SLC2A4RG.H13RSNP.0.PSG.D_meme_format.meme
Transfac format	SLC2A4RG.H13RSNP.0.PSG.D_transfac_format.txt
Homer format	SLC2A4RG.H13RSNP.0.PSG.D_homer_format_0.001.txt SLC2A4RG.H13RSNP.0.PSG.D_homer_format_0.0005.txt SLC2A4RG.H13RSNP.0.PSG.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	96.0	76.0	57.0	81.0
02	22.0	16.0	265.0	7.0
03	1.0	303.0	4.0	2.0
04	1.0	309.0	0.0	0.0
05	0.0	2.0	308.0	0.0
06	1.0	3.0	304.0	2.0
07	0.0	286.0	19.0	5.0
08	8.0	294.0	3.0	5.0
09	1.0	8.0	300.0	1.0
10	0.0	50.0	260.0	0.0

PFM

	A	C	G	T
01	0.31	0.245	0.184	0.261
02	0.071	0.052	0.855	0.023
03	0.003	0.977	0.013	0.006
04	0.003	0.997	0.0	0.0
05	0.0	0.006	0.994	0.0
06	0.003	0.01	0.981	0.006
07	0.0	0.923	0.061	0.016
08	0.026	0.948	0.01	0.016
09	0.003	0.026	0.968	0.003
10	0.0	0.161	0.839	0.0

PWM

	A	C	G	T
01	0.211	-0.019	-0.301	0.043
02	-1.214	-1.51	1.217	-2.236
03	-3.479	1.35	-2.676	-3.135
04	-3.479	1.369	-4.008	-4.008
05	-4.008	-3.135	1.366	-4.008
06	-3.479	-2.879	1.353	-3.135
07	-4.008	1.292	-1.351	-2.507
08	-2.124	1.32	-2.879	-2.507
09	-3.479	-2.124	1.34	-3.479
10	-4.008	-0.428	1.198	-4.008

Standard thresholds

P-value	Threshold
0.001	2.839335
0.0005	3.989105
0.0001	6.702415