SCRT2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SCRT2.H12INVIVO.0.PSM.A
Gene (human)	SCRT2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Scrt2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	vdKCAACAGGTKb
GC content	52.11%
Information content (bits; total / per base)	14.494 / 1.115
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1001

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)	0.977	0.987	0.955	0.975	0.962	0.975	4.554	5.206	473.013	516.237

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.885	0.898	0.807	0.824	0.776	0.791
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	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0
Non-Methyl HT-SELEX, 3 experiments	median	0.77	0.796	0.615	0.649	0.552	0.583
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 2	0.86	0.618	0.909	0.711

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: 2.3.3.2.5
HGNC	HGNC:15952
MGI	MGI:2139287
EntrezGene (human)	GeneID:85508 (SSTAR profile)
EntrezGene (mouse)	GeneID:545474 (SSTAR profile)
UniProt ID (human)	SCRT2_HUMAN
UniProt ID (mouse)	SCRT2_MOUSE
UniProt AC (human)	Q9NQ03 (TFClass)
UniProt AC (mouse)	Q8BTH6 (TFClass)
GRECO-DB-TF	yes

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

PCM	SCRT2.H12INVIVO.0.PSM.A.pcm
PWM	SCRT2.H12INVIVO.0.PSM.A.pwm
PFM	SCRT2.H12INVIVO.0.PSM.A.pfm
Alignment	SCRT2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	SCRT2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	SCRT2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	SCRT2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	SCRT2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	SCRT2.H12INVIVO.0.PSM.A_homer_format_0.001.txt SCRT2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt SCRT2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	401.0	196.0	268.0	136.0
02	426.0	106.0	189.0	280.0
03	58.0	86.0	586.0	271.0
04	18.0	920.0	12.0	51.0
05	842.0	91.0	24.0	44.0
06	969.0	1.0	22.0	9.0
07	1.0	999.0	0.0	1.0
08	994.0	3.0	0.0	4.0
09	143.0	6.0	848.0	4.0
10	11.0	8.0	965.0	17.0
11	10.0	35.0	9.0	947.0
12	105.0	74.0	699.0	123.0
13	144.0	232.0	402.0	223.0

PFM

	A	C	G	T
01	0.401	0.196	0.268	0.136
02	0.426	0.106	0.189	0.28
03	0.058	0.086	0.585	0.271
04	0.018	0.919	0.012	0.051
05	0.841	0.091	0.024	0.044
06	0.968	0.001	0.022	0.009
07	0.001	0.998	0.0	0.001
08	0.993	0.003	0.0	0.004
09	0.143	0.006	0.847	0.004
10	0.011	0.008	0.964	0.017
11	0.01	0.035	0.009	0.946
12	0.105	0.074	0.698	0.123
13	0.144	0.232	0.402	0.223

PWM

	A	C	G	T
01	0.469	-0.242	0.068	-0.604
02	0.529	-0.85	-0.278	0.112
03	-1.44	-1.055	0.847	0.079
04	-2.547	1.297	-2.91	-1.564
05	1.208	-1.0	-2.282	-1.707
06	1.349	-4.526	-2.363	-3.157
07	-4.526	1.379	-4.983	-4.526
08	1.374	-3.976	-4.983	-3.784
09	-0.554	-3.485	1.216	-3.784
10	-2.986	-3.254	1.345	-2.599
11	-3.067	-1.926	-3.157	1.326
12	-0.859	-1.202	1.023	-0.703
13	-0.548	-0.075	0.471	-0.114

Standard thresholds

P-value	Threshold
0.001	2.94096
0.0005	4.165415
0.0001	6.679975