RFX3.H12INVIVO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX3.H12INVIVO.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	12
Consensus	bbGTTGCCWKGG
GC content	58.89%
Information content (bits; total / per base)	13.417 / 1.118
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	1 (7)	0.963	0.967	0.929	0.934	0.951	0.955	4.732	4.804	716.367	728.509
Mouse	1 (5)	0.971	0.974	0.944	0.947	0.961	0.963	5.049	5.085	777.0	863.201

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.734	0.749	0.601	0.625	0.542	0.568
Overall, 6 experiments	best	1.0	0.999	0.999	0.998	0.935	0.942
Methyl HT-SELEX, 1 experiments	median	1.0	0.999	0.999	0.998	0.935	0.942
Methyl HT-SELEX, 1 experiments	best	1.0	0.999	0.999	0.998	0.935	0.942
Non-Methyl HT-SELEX, 5 experiments	median	0.653	0.679	0.563	0.582	0.524	0.543
Non-Methyl HT-SELEX, 5 experiments	best	0.999	0.999	0.998	0.997	0.893	0.907

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.84	0.391	0.786	0.603

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.1.PS.A.pcm
PWM	RFX3.H12INVIVO.1.PS.A.pwm
PFM	RFX3.H12INVIVO.1.PS.A.pfm
Alignment	RFX3.H12INVIVO.1.PS.A.words.tsv
Threshold to P-value map	RFX3.H12INVIVO.1.PS.A.thr
Motif in other formats
JASPAR format	RFX3.H12INVIVO.1.PS.A_jaspar_format.txt
MEME format	RFX3.H12INVIVO.1.PS.A_meme_format.meme
Transfac format	RFX3.H12INVIVO.1.PS.A_transfac_format.txt
Homer format	RFX3.H12INVIVO.1.PS.A_homer_format_0.001.txt RFX3.H12INVIVO.1.PS.A_homer_format_0.0005.txt RFX3.H12INVIVO.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	73.0	493.0	179.0	255.0
02	93.0	258.0	378.0	271.0
03	6.0	6.0	985.0	3.0
04	0.0	9.0	2.0	989.0
05	25.0	67.0	4.0	904.0
06	65.0	23.0	828.0	84.0
07	2.0	920.0	1.0	77.0
08	0.0	744.0	2.0	254.0
09	787.0	50.0	62.0	101.0
10	131.0	40.0	236.0	593.0
11	68.0	6.0	919.0	7.0
12	130.0	62.0	793.0	15.0

PFM

	A	C	G	T
01	0.073	0.493	0.179	0.255
02	0.093	0.258	0.378	0.271
03	0.006	0.006	0.985	0.003
04	0.0	0.009	0.002	0.989
05	0.025	0.067	0.004	0.904
06	0.065	0.023	0.828	0.084
07	0.002	0.92	0.001	0.077
08	0.0	0.744	0.002	0.254
09	0.787	0.05	0.062	0.101
10	0.131	0.04	0.236	0.593
11	0.068	0.006	0.919	0.007
12	0.13	0.062	0.793	0.015

PWM

	A	C	G	T
01	-1.215	0.676	-0.331	0.02
02	-0.977	0.031	0.411	0.08
03	-3.484	-3.484	1.366	-3.975
04	-4.982	-3.156	-4.213	1.37
05	-2.243	-1.298	-3.783	1.28
06	-1.328	-2.32	1.193	-1.077
07	-4.213	1.298	-4.525	-1.162
08	-4.982	1.086	-4.213	0.016
09	1.142	-1.582	-1.374	-0.896
10	-0.64	-1.797	-0.057	0.86
11	-1.284	-3.484	1.297	-3.362
12	-0.648	-1.374	1.15	-2.711

Standard thresholds

P-value	Threshold
0.001	3.55786
0.0005	4.69177
0.0001	7.003435