RFX3.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX3.H12INVIVO.0.PSM.A
Gene (human)	RFX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	14
Consensus	GTTGCCddGRnRMY
GC content	56.71%
Information content (bits; total / per base)	14.389 / 1.028
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	862

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	1 (7)	0.971	0.974	0.946	0.949	0.961	0.965	6.003	6.047	747.658	760.886
Mouse	1 (5)	0.975	0.977	0.955	0.957	0.965	0.967	6.284	6.309	791.032	891.237

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.717	0.738	0.587	0.617	0.536	0.564
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	0.93	0.94
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	1.0	0.93	0.94
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	0.93	0.94
Non-Methyl HT-SELEX, 5 experiments	median	0.656	0.682	0.564	0.588	0.53	0.549
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	1.0	1.0	0.891	0.908

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.777	0.375	0.772	0.565

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Fork head/winged helix factors {3.3} (TFClass)
TF family	RFX {3.3.3} (TFClass)
TF subfamily	{3.3.3.0} (TFClass)
TFClass ID	TFClass: 3.3.3.0.3
HGNC	HGNC:9984
MGI	MGI:106582
EntrezGene (human)	GeneID:5991 (SSTAR profile)
EntrezGene (mouse)	GeneID:19726 (SSTAR profile)
UniProt ID (human)	RFX3_HUMAN
UniProt ID (mouse)	RFX3_MOUSE
UniProt AC (human)	P48380 (TFClass)
UniProt AC (mouse)	P48381 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 1 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	RFX3.H12INVIVO.0.PSM.A.pcm
PWM	RFX3.H12INVIVO.0.PSM.A.pwm
PFM	RFX3.H12INVIVO.0.PSM.A.pfm
Alignment	RFX3.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	RFX3.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	RFX3.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	RFX3.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	RFX3.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	RFX3.H12INVIVO.0.PSM.A_homer_format_0.001.txt RFX3.H12INVIVO.0.PSM.A_homer_format_0.0005.txt RFX3.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	7.0	5.0	849.0	1.0
02	5.0	33.0	4.0	820.0
03	16.0	84.0	13.0	749.0
04	75.0	7.0	728.0	52.0
05	0.0	803.0	3.0	56.0
06	6.0	620.0	3.0	233.0
07	663.0	47.0	76.0	76.0
08	138.0	40.0	207.0	477.0
09	38.0	9.0	805.0	10.0
10	117.0	68.0	663.0	14.0
11	239.0	292.0	199.0	132.0
12	431.0	54.0	309.0	68.0
13	596.0	171.0	62.0	33.0
14	70.0	621.0	69.0	102.0

PFM

	A	C	G	T
01	0.008	0.006	0.985	0.001
02	0.006	0.038	0.005	0.951
03	0.019	0.097	0.015	0.869
04	0.087	0.008	0.845	0.06
05	0.0	0.932	0.003	0.065
06	0.007	0.719	0.003	0.27
07	0.769	0.055	0.088	0.088
08	0.16	0.046	0.24	0.553
09	0.044	0.01	0.934	0.012
10	0.136	0.079	0.769	0.016
11	0.277	0.339	0.231	0.153
12	0.5	0.063	0.358	0.079
13	0.691	0.198	0.072	0.038
14	0.081	0.72	0.08	0.118

PWM

	A	C	G	T
01	-3.219	-3.48	1.365	-4.391
02	-3.48	-1.834	-3.642	1.331
03	-2.508	-0.93	-2.694	1.24
04	-1.041	-3.219	1.212	-1.398
05	-4.856	1.31	-3.835	-1.326
06	-3.341	1.052	-3.835	0.077
07	1.119	-1.495	-1.028	-1.028
08	-0.441	-1.651	-0.04	0.79
09	-1.7	-3.011	1.312	-2.922
10	-0.604	-1.137	1.119	-2.628
11	0.103	0.302	-0.079	-0.485
12	0.689	-1.361	0.358	-1.137
13	1.012	-0.229	-1.227	-1.834
14	-1.108	1.053	-1.122	-0.739

Standard thresholds

P-value	Threshold
0.001	3.32466
0.0005	4.44571
0.0001	6.75341