SCRT1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SCRT1.H12INVITRO.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	dhKCAACAGGTKn
GC content	50.36%
Information content (bits; total / per base)	17.807 / 1.37
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	837

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)	0.709	0.865	0.692	0.87	0.929	0.978	4.261	5.874	306.415	805.076

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.83	0.842	0.792	0.798	0.773	0.778
Overall, 4 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	0.999	0.998	0.997
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	0.999	0.998	0.997
Non-Methyl HT-SELEX, 3 experiments	median	0.661	0.684	0.583	0.596	0.548	0.558
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.988	0.834	0.951	0.651
batch 2	0.89	0.801	0.909	0.706

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.H12INVITRO.0.PSM.A.pcm
PWM	SCRT1.H12INVITRO.0.PSM.A.pwm
PFM	SCRT1.H12INVITRO.0.PSM.A.pfm
Alignment	SCRT1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	SCRT1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	SCRT1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	SCRT1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	SCRT1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	SCRT1.H12INVITRO.0.PSM.A_homer_format_0.001.txt SCRT1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt SCRT1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	317.25	125.25	256.25	138.25
02	307.75	111.75	81.75	335.75
03	14.0	3.0	540.0	280.0
04	0.0	837.0	0.0	0.0
05	837.0	0.0	0.0	0.0
06	837.0	0.0	0.0	0.0
07	0.0	837.0	0.0	0.0
08	837.0	0.0	0.0	0.0
09	0.0	0.0	837.0	0.0
10	0.0	0.0	837.0	0.0
11	0.0	0.0	0.0	837.0
12	128.0	41.0	505.0	163.0
13	148.75	157.75	309.75	220.75

PFM

	A	C	G	T
01	0.379	0.15	0.306	0.165
02	0.368	0.134	0.098	0.401
03	0.017	0.004	0.645	0.335
04	0.0	1.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	1.0	0.0	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.0	1.0	0.0
10	0.0	0.0	1.0	0.0
11	0.0	0.0	0.0	1.0
12	0.153	0.049	0.603	0.195
13	0.178	0.188	0.37	0.264

PWM

	A	C	G	T
01	0.413	-0.508	0.201	-0.41
02	0.383	-0.62	-0.928	0.47
03	-2.599	-3.808	0.943	0.289
04	-4.831	1.38	-4.831	-4.831
05	1.38	-4.831	-4.831	-4.831
06	1.38	-4.831	-4.831	-4.831
07	-4.831	1.38	-4.831	-4.831
08	1.38	-4.831	-4.831	-4.831
09	-4.831	-4.831	1.38	-4.831
10	-4.831	-4.831	1.38	-4.831
11	-4.831	-4.831	-4.831	1.38
12	-0.486	-1.598	0.876	-0.248
13	-0.338	-0.28	0.39	0.053

Standard thresholds

P-value	Threshold
0.001	-0.892295
0.0005	0.243815
0.0001	4.91822