SCRT1.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SCRT1.H12CORE.0.PSM.A
Gene (human)	SCRT1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Scrt1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	vdKCAACAGGTKb
GC content	50.2%
Information content (bits; total / per base)	15.933 / 1.226
Data sources	ChIP-Seq + HT-SELEX + Methyl-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	2 (12)	0.963	0.994	0.939	0.991	0.951	0.988	4.576	6.295	327.264	813.292

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.827	0.84	0.787	0.795	0.77	0.776
Overall, 4 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	0.999	0.999	0.998
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	0.999	0.999	0.998
Non-Methyl HT-SELEX, 3 experiments	median	0.654	0.68	0.573	0.591	0.54	0.554
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.984	0.728	0.948	0.65
batch 2	0.914	0.786	0.908	0.642

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	More than 3 adjacent zinc fingers {2.3.3} (TFClass)
TF subfamily	Snail-like {2.3.3.2} (TFClass)
TFClass ID	TFClass: 2.3.3.2.4
HGNC	HGNC:15950
MGI	MGI:2176606
EntrezGene (human)	GeneID:83482 (SSTAR profile)
EntrezGene (mouse)	GeneID:170729 (SSTAR profile)
UniProt ID (human)	SCRT1_HUMAN
UniProt ID (mouse)	SCRT1_MOUSE
UniProt AC (human)	Q9BWW7 (TFClass)
UniProt AC (mouse)	Q99M85 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	SCRT1.H12CORE.0.PSM.A.pcm
PWM	SCRT1.H12CORE.0.PSM.A.pwm
PFM	SCRT1.H12CORE.0.PSM.A.pfm
Alignment	SCRT1.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	SCRT1.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	SCRT1.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	SCRT1.H12CORE.0.PSM.A_meme_format.meme
Transfac format	SCRT1.H12CORE.0.PSM.A_transfac_format.txt
Homer format	SCRT1.H12CORE.0.PSM.A_homer_format_0.001.txt SCRT1.H12CORE.0.PSM.A_homer_format_0.0005.txt SCRT1.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	509.0	141.0	249.0	101.0
02	359.0	92.0	118.0	431.0
03	9.25	37.25	498.25	455.25
04	1.25	983.25	5.25	10.25
05	849.25	98.25	36.25	16.25
06	975.25	0.25	13.25	11.25
07	0.25	999.25	0.25	0.25
08	993.25	0.25	1.25	5.25
09	115.25	7.25	876.25	1.25
10	9.25	5.25	973.25	12.25
11	3.25	13.25	3.25	980.25
12	71.25	66.25	721.25	141.25
13	157.25	179.25	408.25	255.25

PFM

	A	C	G	T
01	0.509	0.141	0.249	0.101
02	0.359	0.092	0.118	0.431
03	0.009	0.037	0.498	0.455
04	0.001	0.983	0.005	0.01
05	0.849	0.098	0.036	0.016
06	0.975	0.0	0.013	0.011
07	0.0	0.999	0.0	0.0
08	0.993	0.0	0.001	0.005
09	0.115	0.007	0.876	0.001
10	0.009	0.005	0.973	0.012
11	0.003	0.013	0.003	0.98
12	0.071	0.066	0.721	0.141
13	0.157	0.179	0.408	0.255

PWM

	A	C	G	T
01	0.707	-0.567	-0.004	-0.896
02	0.36	-0.988	-0.743	0.542
03	-3.133	-1.865	0.686	0.596
04	-4.437	1.364	-3.586	-3.045
05	1.218	-0.923	-1.891	-2.639
06	1.356	-4.847	-2.822	-2.965
07	-4.847	1.38	-4.847	-4.847
08	1.374	-4.847	-4.437	-3.586
09	-0.766	-3.334	1.249	-4.437
10	-3.133	-3.586	1.354	-2.891
11	-3.924	-2.822	-3.924	1.361
12	-1.238	-1.309	1.055	-0.566
13	-0.46	-0.33	0.488	0.021

Standard thresholds

P-value	Threshold
0.001	1.87026
0.0005	3.24886
0.0001	6.107075