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

Motif	GABPA.H12INVIVO.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	14
Consensus	vvnvSCGGAAGTdv
GC content	61.9%
Information content (bits; total / per base)	14.029 / 1.002
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	36 (228)	0.969	0.983	0.935	0.964	0.952	0.973	4.463	5.053	352.288	458.027
Mouse	5 (33)	0.975	0.99	0.946	0.977	0.962	0.975	4.622	4.937	276.699	441.032

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.998	0.997	0.997	0.996	0.995	0.992
Overall, 2 experiments	best	0.999	0.998	0.998	0.997	0.997	0.996
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.998	0.997	0.997	0.996
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.998	0.997	0.997	0.996
Non-Methyl HT-SELEX, 1 experiments	median	0.998	0.996	0.996	0.994	0.993	0.989
Non-Methyl HT-SELEX, 1 experiments	best	0.998	0.996	0.996	0.994	0.993	0.989

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.788	9.019	0.228	0.157

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

PCM

	A	C	G	T
01	137.0	245.0	486.0	133.0
02	207.0	254.0	453.0	87.0
03	343.0	274.0	257.0	127.0
04	458.0	172.0	319.0	52.0
05	74.0	753.0	172.0	2.0
06	90.0	905.0	6.0	0.0
07	1.0	1.0	999.0	0.0
08	3.0	0.0	998.0	0.0
09	998.0	2.0	0.0	1.0
10	986.0	1.0	0.0	14.0
11	108.0	17.0	875.0	1.0
12	24.0	155.0	19.0	803.0
13	158.0	128.0	583.0	132.0
14	314.0	260.0	341.0	86.0

PFM

	A	C	G	T
01	0.137	0.245	0.486	0.133
02	0.207	0.254	0.453	0.087
03	0.343	0.274	0.257	0.127
04	0.458	0.172	0.319	0.052
05	0.074	0.752	0.172	0.002
06	0.09	0.904	0.006	0.0
07	0.001	0.001	0.998	0.0
08	0.003	0.0	0.997	0.0
09	0.997	0.002	0.0	0.001
10	0.985	0.001	0.0	0.014
11	0.108	0.017	0.874	0.001
12	0.024	0.155	0.019	0.802
13	0.158	0.128	0.582	0.132
14	0.314	0.26	0.341	0.086

PWM

	A	C	G	T
01	-0.597	-0.021	0.66	-0.626
02	-0.188	0.015	0.59	-1.044
03	0.313	0.09	0.026	-0.672
04	0.601	-0.372	0.241	-1.545
05	-1.202	1.097	-0.372	-4.214
06	-1.011	1.281	-3.485	-4.983
07	-4.526	-4.526	1.379	-4.983
08	-3.976	-4.983	1.378	-4.983
09	1.378	-4.214	-4.983	-4.526
10	1.366	-4.526	-4.983	-2.774
11	-0.831	-2.599	1.247	-4.526
12	-2.282	-0.475	-2.498	1.161
13	-0.456	-0.664	0.842	-0.634
14	0.226	0.038	0.308	-1.055

Standard thresholds

P-value	Threshold
0.001	2.86976
0.0005	4.17631
0.0001	6.90946