SCRT2.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SCRT2.H12INVITRO.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	vhGCAACAGGTGn
GC content	57.2%
Information content (bits; total / per base)	20.08 / 1.545
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	985

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)	0.576	0.613	0.499	0.56	0.913	0.932	3.861	4.382	393.022	461.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.899	0.906	0.821	0.832	0.787	0.798
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	1.0	1.0	0.999
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999
Non-Methyl HT-SELEX, 3 experiments	median	0.797	0.811	0.641	0.665	0.575	0.597
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 2	0.794	0.739	0.904	0.79

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.H12INVITRO.0.PSM.A.pcm
PWM	SCRT2.H12INVITRO.0.PSM.A.pwm
PFM	SCRT2.H12INVITRO.0.PSM.A.pfm
Alignment	SCRT2.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	SCRT2.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	SCRT2.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	SCRT2.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	SCRT2.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	SCRT2.H12INVITRO.0.PSM.A_homer_format_0.001.txt SCRT2.H12INVITRO.0.PSM.A_homer_format_0.0005.txt SCRT2.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	302.25	157.25	376.25	149.25
02	306.25	246.25	113.25	319.25
03	0.0	0.0	985.0	0.0
04	0.0	985.0	0.0	0.0
05	985.0	0.0	0.0	0.0
06	985.0	0.0	0.0	0.0
07	0.0	985.0	0.0	0.0
08	985.0	0.0	0.0	0.0
09	0.0	0.0	985.0	0.0
10	0.0	0.0	985.0	0.0
11	0.0	0.0	0.0	985.0
12	0.0	0.0	967.0	18.0
13	201.0	262.0	277.0	245.0

PFM

	A	C	G	T
01	0.307	0.16	0.382	0.152
02	0.311	0.25	0.115	0.324
03	0.0	0.0	1.0	0.0
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	0.0	0.0	0.982	0.018
13	0.204	0.266	0.281	0.249

PWM

	A	C	G	T
01	0.204	-0.445	0.422	-0.496
02	0.217	0.0	-0.769	0.258
03	-4.969	-4.969	1.381	-4.969
04	-4.969	1.381	-4.969	-4.969
05	1.381	-4.969	-4.969	-4.969
06	1.381	-4.969	-4.969	-4.969
07	-4.969	1.381	-4.969	-4.969
08	1.381	-4.969	-4.969	-4.969
09	-4.969	-4.969	1.381	-4.969
10	-4.969	-4.969	1.381	-4.969
11	-4.969	-4.969	-4.969	1.381
12	-4.969	-4.969	1.363	-2.532
13	-0.201	0.062	0.117	-0.005

Standard thresholds

P-value	Threshold
0.001	-4.68819
0.0005	-2.501545
0.0001	1.630325