SCRT2.H14RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SCRT2.H14RSNP.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	16
Consensus	dhGCAACAGGTGbnnn
GC content	54.28%
Information content (bits; total / per base)	18.332 / 1.146
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	468
Previous names	SCRT2.H12RSNP.0.PSM.A

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)	0.857	0.894	0.842	0.889	0.944	0.961	4.24	4.844	434.481	493.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.888	0.898	0.811	0.826	0.779	0.793
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	0.776	0.796	0.622	0.652	0.559	0.586
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	0.893	0.768	0.925	0.812

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	SCRT2.H14RSNP.0.PSM.A.pcm
PWM	SCRT2.H14RSNP.0.PSM.A.pwm
PFM	SCRT2.H14RSNP.0.PSM.A.pfm
Threshold to P-value map	SCRT2.H14RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	SCRT2.H14RSNP.0.PSM.A_jaspar_format.txt
MEME format	SCRT2.H14RSNP.0.PSM.A_meme_format.meme
Transfac format	SCRT2.H14RSNP.0.PSM.A_transfac_format.txt
Homer format	SCRT2.H14RSNP.0.PSM.A_homer_format_0.001.txt SCRT2.H14RSNP.0.PSM.A_homer_format_0.0005.txt SCRT2.H14RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	140.75	49.75	219.75	57.75
02	156.0	113.0	45.0	154.0
03	7.0	11.0	379.0	71.0
04	1.0	454.0	9.0	4.0
05	462.0	1.0	1.0	4.0
06	466.0	0.0	2.0	0.0
07	0.0	468.0	0.0	0.0
08	468.0	0.0	0.0	0.0
09	0.0	0.0	468.0	0.0
10	0.0	0.0	468.0	0.0
11	1.0	0.0	1.0	466.0
12	21.0	11.0	387.0	49.0
13	78.0	104.0	192.0	94.0
14	145.0	103.0	104.0	116.0
15	99.75	142.75	83.75	141.75
16	94.25	136.25	111.25	126.25

PFM

	A	C	G	T
01	0.301	0.106	0.47	0.123
02	0.333	0.241	0.096	0.329
03	0.015	0.024	0.81	0.152
04	0.002	0.97	0.019	0.009
05	0.987	0.002	0.002	0.009
06	0.996	0.0	0.004	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	0.002	0.0	0.002	0.996
12	0.045	0.024	0.827	0.105
13	0.167	0.222	0.41	0.201
14	0.31	0.22	0.222	0.248
15	0.213	0.305	0.179	0.303
16	0.201	0.291	0.238	0.27

PWM

	A	C	G	T
01	0.183	-0.838	0.624	-0.693
02	0.284	-0.034	-0.935	0.272
03	-2.631	-2.247	1.166	-0.491
04	-3.844	1.346	-2.42	-3.064
05	1.364	-3.844	-3.844	-3.064
06	1.372	-4.345	-3.512	-4.345
07	-4.345	1.377	-4.345	-4.345
08	1.377	-4.345	-4.345	-4.345
09	-4.345	-4.345	1.377	-4.345
10	-4.345	-4.345	1.377	-4.345
11	-3.844	-4.345	-3.844	1.372
12	-1.66	-2.247	1.187	-0.853
13	-0.399	-0.116	0.49	-0.216
14	0.212	-0.126	-0.116	-0.008
15	-0.157	0.197	-0.329	0.19
16	-0.213	0.15	-0.05	0.075

Standard thresholds

P-value	Threshold
0.001	0.14861
0.0005	1.69191
0.0001	4.96181