YBOX1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	YBOX1.H12INVIVO.0.SM.D
Gene (human)	YBX1 (GeneCards)
Gene synonyms (human)	NSEP1, YB1
Gene (mouse)	Ybx1
Gene synonyms (mouse)	Msy-1, Msy1, Nsep1, Yb1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nhKTWCCATChhn
GC content	49.93%
Information content (bits; total / per base)	12.972 / 0.998
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7092

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.949	0.928	0.882	0.853	0.78	0.763
Overall, 3 experiments	best	0.958	0.939	0.911	0.882	0.829	0.804
Methyl HT-SELEX, 1 experiments	median	0.856	0.807	0.789	0.741	0.712	0.68
Methyl HT-SELEX, 1 experiments	best	0.856	0.807	0.789	0.741	0.712	0.68
Non-Methyl HT-SELEX, 2 experiments	median	0.954	0.934	0.896	0.867	0.805	0.783
Non-Methyl HT-SELEX, 2 experiments	best	0.958	0.939	0.911	0.882	0.829	0.804

TF superclass	beta-Barrel DNA-binding domains {9} (TFClass)
TF class	Cold-shock domain factors {9.1} (TFClass)
TF family	Dbp {9.1.1} (TFClass)
TF subfamily	B {9.1.1.2} (TFClass)
TFClass ID	TFClass: 9.1.1.2.1
HGNC	HGNC:8014
MGI	MGI:99146
EntrezGene (human)	GeneID:4904 (SSTAR profile)
EntrezGene (mouse)	GeneID:22608 (SSTAR profile)
UniProt ID (human)	YBOX1_HUMAN
UniProt ID (mouse)	YBOX1_MOUSE
UniProt AC (human)	P67809 (TFClass)
UniProt AC (mouse)	P62960 (TFClass)
GRECO-DB-TF	no

ChIP-Seq	0 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	1

PCM	YBOX1.H12INVIVO.0.SM.D.pcm
PWM	YBOX1.H12INVIVO.0.SM.D.pwm
PFM	YBOX1.H12INVIVO.0.SM.D.pfm
Alignment	YBOX1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	YBOX1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	YBOX1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	YBOX1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	YBOX1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	YBOX1.H12INVIVO.0.SM.D_homer_format_0.001.txt YBOX1.H12INVIVO.0.SM.D_homer_format_0.0005.txt YBOX1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1563.5	2226.5	1307.5	1994.5
02	1046.5	3015.5	687.5	2342.5
03	347.0	606.0	5444.0	695.0
04	91.0	958.0	29.0	6014.0
05	4327.0	116.0	15.0	2634.0
06	382.0	6697.0	0.0	13.0
07	0.0	7043.0	0.0	49.0
08	7086.0	0.0	0.0	6.0
09	0.0	763.0	0.0	6329.0
10	0.0	7091.0	1.0	0.0
11	1449.0	3415.0	311.0	1917.0
12	1836.75	2126.75	556.75	2571.75
13	1309.5	2432.5	1190.5	2159.5

PFM

	A	C	G	T
01	0.22	0.314	0.184	0.281
02	0.148	0.425	0.097	0.33
03	0.049	0.085	0.768	0.098
04	0.013	0.135	0.004	0.848
05	0.61	0.016	0.002	0.371
06	0.054	0.944	0.0	0.002
07	0.0	0.993	0.0	0.007
08	0.999	0.0	0.0	0.001
09	0.0	0.108	0.0	0.892
10	0.0	1.0	0.0	0.0
11	0.204	0.482	0.044	0.27
12	0.259	0.3	0.079	0.363
13	0.185	0.343	0.168	0.304

PWM

	A	C	G	T
01	-0.126	0.228	-0.304	0.118
02	-0.526	0.531	-0.945	0.278
03	-1.626	-1.071	1.121	-0.935
04	-2.947	-0.615	-4.041	1.221
05	0.891	-2.709	-4.636	0.395
06	-1.53	1.328	-6.686	-4.759
07	-6.686	1.378	-6.686	-3.546
08	1.385	-6.686	-6.686	-5.376
09	-6.686	-0.842	-6.686	1.272
10	-6.686	1.385	-6.313	-6.686
11	-0.202	0.655	-1.735	0.078
12	0.035	0.182	-1.156	0.372
13	-0.303	0.316	-0.398	0.197

Standard thresholds

P-value	Threshold
0.001	2.92616
0.0005	4.484215
0.0001	7.306865