RFX3.H12INVITRO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX3.H12INVITRO.1.PS.A
Gene (human)	RFX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	14
Consensus	nbGTTRCCATGGnd
GC content	52.3%
Information content (bits; total / per base)	14.624 / 1.045
Data sources	ChIP-Seq + HT-SELEX
Aligned words	9946

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)	0.959	0.964	0.925	0.93	0.95	0.955	5.129	5.222	704.638	714.886
Mouse	1 (5)	0.963	0.963	0.933	0.934	0.955	0.956	5.314	5.352	727.745	816.796

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.737	0.751	0.607	0.628	0.548	0.572
Overall, 6 experiments	best	1.0	1.0	1.0	0.999	0.935	0.942
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	0.999	0.935	0.942
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	0.999	0.935	0.942
Non-Methyl HT-SELEX, 5 experiments	median	0.66	0.679	0.571	0.586	0.531	0.548
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	0.999	0.999	0.899	0.913

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.754	0.444	0.752	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.H12INVITRO.1.PS.A.pcm
PWM	RFX3.H12INVITRO.1.PS.A.pwm
PFM	RFX3.H12INVITRO.1.PS.A.pfm
Alignment	RFX3.H12INVITRO.1.PS.A.words.tsv
Threshold to P-value map	RFX3.H12INVITRO.1.PS.A.thr
Motif in other formats
JASPAR format	RFX3.H12INVITRO.1.PS.A_jaspar_format.txt
MEME format	RFX3.H12INVITRO.1.PS.A_meme_format.meme
Transfac format	RFX3.H12INVITRO.1.PS.A_transfac_format.txt
Homer format	RFX3.H12INVITRO.1.PS.A_homer_format_0.001.txt RFX3.H12INVITRO.1.PS.A_homer_format_0.0005.txt RFX3.H12INVITRO.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1402.25	3517.25	2181.25	2845.25
02	824.75	4254.75	3121.75	1744.75
03	86.0	12.0	9813.0	35.0
04	7.0	36.0	17.0	9886.0
05	600.0	200.0	4.0	9142.0
06	1928.0	19.0	7484.0	515.0
07	1.0	9099.0	14.0	832.0
08	2.0	6611.0	15.0	3318.0
09	9552.0	66.0	97.0	231.0
10	726.0	252.0	848.0	8120.0
11	979.0	164.0	8692.0	111.0
12	857.0	778.0	8013.0	298.0
13	2755.25	2655.25	1495.25	3040.25
14	4630.5	788.5	2582.5	1944.5

PFM

	A	C	G	T
01	0.141	0.354	0.219	0.286
02	0.083	0.428	0.314	0.175
03	0.009	0.001	0.987	0.004
04	0.001	0.004	0.002	0.994
05	0.06	0.02	0.0	0.919
06	0.194	0.002	0.752	0.052
07	0.0	0.915	0.001	0.084
08	0.0	0.665	0.002	0.334
09	0.96	0.007	0.01	0.023
10	0.073	0.025	0.085	0.816
11	0.098	0.016	0.874	0.011
12	0.086	0.078	0.806	0.03
13	0.277	0.267	0.15	0.306
14	0.466	0.079	0.26	0.196

PWM

	A	C	G	T
01	-0.572	0.347	-0.131	0.135
02	-1.102	0.537	0.227	-0.354
03	-3.339	-5.159	1.372	-4.201
04	-5.589	-4.174	-4.859	1.38
05	-1.419	-2.51	-5.979	1.301
06	-0.254	-4.761	1.101	-1.571
07	-6.625	1.297	-5.028	-1.093
08	-6.361	0.977	-4.969	0.288
09	1.345	-3.596	-3.221	-2.367
10	-1.229	-2.281	-1.074	1.183
11	-0.931	-2.706	1.251	-3.09
12	-1.063	-1.16	1.17	-2.115
13	0.103	0.066	-0.508	0.201
14	0.621	-1.147	0.038	-0.246

Standard thresholds

P-value	Threshold
0.001	2.61876
0.0005	3.93011
0.0001	6.608765