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

Motif	GABPA.H12CORE.0.PSM.A
Gene (human)	GABPA (GeneCards)
Gene synonyms (human)	E4TF1A
Gene (mouse)	Gabpa
Gene synonyms (mouse)	E4tf1a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nRCCGGAAGYdn
GC content	55.45%
Information content (bits; total / per base)	14.285 / 1.19
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9955

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	36 (228)	0.966	0.981	0.928	0.968	0.945	0.969	4.124	4.662	331.171	437.328
Mouse	5 (33)	0.971	0.985	0.935	0.958	0.959	0.971	4.379	4.792	260.377	405.301

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.999	0.998	0.999	0.998	0.997	0.995
Overall, 2 experiments	best	0.999	0.999	0.999	0.998	0.998	0.997
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.999	0.998	0.998	0.997
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.999	0.998	0.998	0.997
Non-Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.998	0.997	0.995	0.993
Non-Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.998	0.997	0.995	0.993

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	6.182	11.081	0.254	0.197

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Tryptophan cluster factors {3.5} (TFClass)
TF family	Ets-related {3.5.2} (TFClass)
TF subfamily	ETS-like {3.5.2.1} (TFClass)
TFClass ID	TFClass: 3.5.2.1.5
HGNC	HGNC:4071
MGI	MGI:95610
EntrezGene (human)	GeneID:2551 (SSTAR profile)
EntrezGene (mouse)	GeneID:14390 (SSTAR profile)
UniProt ID (human)	GABPA_HUMAN
UniProt ID (mouse)	GABPA_MOUSE
UniProt AC (human)	Q06546 (TFClass)
UniProt AC (mouse)	Q00422 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	36 human, 5 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

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

PCM

	A	C	G	T
01	3552.0	2049.0	2305.0	2049.0
02	7540.5	193.5	1273.5	947.5
03	273.0	9033.0	622.0	27.0
04	878.0	9069.0	3.0	5.0
05	0.0	1.0	9954.0	0.0
06	0.0	0.0	9955.0	0.0
07	9955.0	0.0	0.0	0.0
08	9721.0	0.0	0.0	234.0
09	1185.0	89.0	8680.0	1.0
10	171.0	1681.0	580.0	7523.0
11	3285.0	1277.0	3774.0	1619.0
12	2788.0	2621.0	3077.0	1469.0

PFM

	A	C	G	T
01	0.357	0.206	0.232	0.206
02	0.757	0.019	0.128	0.095
03	0.027	0.907	0.062	0.003
04	0.088	0.911	0.0	0.001
05	0.0	0.0	1.0	0.0
06	0.0	0.0	1.0	0.0
07	1.0	0.0	0.0	0.0
08	0.976	0.0	0.0	0.024
09	0.119	0.009	0.872	0.0
10	0.017	0.169	0.058	0.756
11	0.33	0.128	0.379	0.163
12	0.28	0.263	0.309	0.148

PWM

	A	C	G	T
01	0.355	-0.194	-0.077	-0.194
02	1.108	-2.543	-0.669	-0.964
03	-2.203	1.288	-1.384	-4.443
04	-1.04	1.292	-6.152	-5.832
05	-6.987	-6.626	1.386	-6.987
06	-6.987	-6.987	1.386	-6.987
07	1.386	-6.987	-6.987	-6.987
08	1.362	-6.987	-6.987	-2.355
09	-0.741	-3.306	1.249	-6.626
10	-2.665	-0.392	-1.453	1.106
11	0.277	-0.666	0.416	-0.429
12	0.113	0.052	0.212	-0.527

Standard thresholds

P-value	Threshold
0.001	1.66983
0.0005	3.463435
0.0001	6.75784