RFX4.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX4.H12INVIVO.0.SM.D
Gene (human)	RFX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx4
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	16
Consensus	bGTTGCCAKGRhdMYv
GC content	52.99%
Information content (bits; total / per base)	14.403 / 0.9
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9672

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.989	0.987	0.855	0.857	0.705	0.728
Overall, 5 experiments	best	1.0	1.0	1.0	1.0	0.997	0.997
Methyl HT-SELEX, 2 experiments	median	0.994	0.993	0.926	0.928	0.843	0.859
Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	1.0	0.997	0.997
Non-Methyl HT-SELEX, 3 experiments	median	0.988	0.986	0.855	0.857	0.705	0.728
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	1.0	0.997	0.997

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: 3.3.3.0.4
HGNC	HGNC:9985
MGI	MGI:1918387
EntrezGene (human)	GeneID:5992 (SSTAR profile)
EntrezGene (mouse)	GeneID:71137 (SSTAR profile)
UniProt ID (human)	RFX4_HUMAN
UniProt ID (mouse)	RFX4_MOUSE
UniProt AC (human)	Q33E94 (TFClass)
UniProt AC (mouse)	Q7TNK1 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	2

PCM	RFX4.H12INVIVO.0.SM.D.pcm
PWM	RFX4.H12INVIVO.0.SM.D.pwm
PFM	RFX4.H12INVIVO.0.SM.D.pfm
Alignment	RFX4.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	RFX4.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	RFX4.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	RFX4.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	RFX4.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	RFX4.H12INVIVO.0.SM.D_homer_format_0.001.txt RFX4.H12INVIVO.0.SM.D_homer_format_0.0005.txt RFX4.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1122.5	3602.5	3159.5	1787.5
02	160.0	109.0	9323.0	80.0
03	80.0	371.0	92.0	9129.0
04	994.0	223.0	68.0	8387.0
05	1644.0	29.0	7756.0	243.0
06	5.0	8544.0	23.0	1100.0
07	19.0	7207.0	90.0	2356.0
08	8345.0	239.0	461.0	627.0
09	871.0	373.0	1381.0	7047.0
10	739.0	161.0	8642.0	130.0
11	1582.0	1235.0	6384.0	471.0
12	2241.0	2772.0	762.0	3897.0
13	4871.0	420.0	1794.0	2587.0
14	6492.0	2009.0	542.0	629.0
15	735.5	6855.5	925.5	1155.5
16	1768.5	2984.5	3469.5	1449.5

PFM

	A	C	G	T
01	0.116	0.372	0.327	0.185
02	0.017	0.011	0.964	0.008
03	0.008	0.038	0.01	0.944
04	0.103	0.023	0.007	0.867
05	0.17	0.003	0.802	0.025
06	0.001	0.883	0.002	0.114
07	0.002	0.745	0.009	0.244
08	0.863	0.025	0.048	0.065
09	0.09	0.039	0.143	0.729
10	0.076	0.017	0.894	0.013
11	0.164	0.128	0.66	0.049
12	0.232	0.287	0.079	0.403
13	0.504	0.043	0.185	0.267
14	0.671	0.208	0.056	0.065
15	0.076	0.709	0.096	0.119
16	0.183	0.309	0.359	0.15

PWM

	A	C	G	T
01	-0.766	0.398	0.267	-0.302
02	-2.702	-3.079	1.349	-3.381
03	-3.381	-1.869	-3.245	1.328
04	-0.888	-2.374	-3.539	1.243
05	-0.385	-4.348	1.165	-2.289
06	-5.805	1.262	-4.561	-0.786
07	-4.733	1.091	-3.267	-0.026
08	1.238	-2.306	-1.653	-1.347
09	-1.019	-1.864	-0.559	1.069
10	-1.183	-2.696	1.273	-2.907
11	-0.424	-0.671	0.97	-1.632
12	-0.076	0.137	-1.153	0.477
13	0.7	-1.746	-0.298	0.067
14	0.987	-0.185	-1.492	-1.344
15	-1.188	1.041	-0.959	-0.737
16	-0.312	0.21	0.361	-0.511

Standard thresholds

P-value	Threshold
0.001	3.25331
0.0005	4.37091
0.0001	6.69501