ATF4.H12RSNP.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ATF4.H12RSNP.2.SM.B
Gene (human)	ATF4 (GeneCards)
Gene synonyms (human)	CREB2, TXREB
Gene (mouse)	Atf4
Gene synonyms (mouse)	Creb2
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	17
Consensus	nhRRMTGACGTCATMhn
GC content	45.29%
Information content (bits; total / per base)	19.98 / 1.175
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9156

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	7 (42)	0.599	0.69	0.443	0.57	0.629	0.68	1.404	1.675	68.745	141.638
Mouse	2 (9)	0.622	0.643	0.469	0.491	0.608	0.616	1.437	1.49	48.509	64.187

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.776	0.761	0.628	0.642	0.556	0.58
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.999	0.999	0.914	0.918
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.999	0.999	0.914	0.918
Non-Methyl HT-SELEX, 5 experiments	median	0.64	0.601	0.576	0.563	0.539	0.539
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.377	4.215	0.223	0.175

TF superclass	Basic domains {1} (TFClass)
TF class	Basic leucine zipper factors (bZIP) {1.1} (TFClass)
TF family	ATF4-related {1.1.6} (TFClass)
TF subfamily	{1.1.6.0} (TFClass)
TFClass ID	TFClass: 1.1.6.0.1
HGNC	HGNC:786
MGI	MGI:88096
EntrezGene (human)	GeneID:468 (SSTAR profile)
EntrezGene (mouse)	GeneID:11911 (SSTAR profile)
UniProt ID (human)	ATF4_HUMAN
UniProt ID (mouse)	ATF4_MOUSE
UniProt AC (human)	P18848 (TFClass)
UniProt AC (mouse)	Q06507 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	7 human, 2 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	ATF4.H12RSNP.2.SM.B.pcm
PWM	ATF4.H12RSNP.2.SM.B.pwm
PFM	ATF4.H12RSNP.2.SM.B.pfm
Alignment	ATF4.H12RSNP.2.SM.B.words.tsv
Threshold to P-value map	ATF4.H12RSNP.2.SM.B.thr
Motif in other formats
JASPAR format	ATF4.H12RSNP.2.SM.B_jaspar_format.txt
MEME format	ATF4.H12RSNP.2.SM.B_meme_format.meme
Transfac format	ATF4.H12RSNP.2.SM.B_transfac_format.txt
Homer format	ATF4.H12RSNP.2.SM.B_homer_format_0.001.txt ATF4.H12RSNP.2.SM.B_homer_format_0.0005.txt ATF4.H12RSNP.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2683.25	1715.25	2117.25	2640.25
02	3324.0	1296.0	1203.0	3333.0
03	2348.0	175.0	5494.0	1139.0
04	961.0	137.0	7171.0	887.0
05	6290.0	2519.0	344.0	3.0
06	1.0	0.0	2.0	9153.0
07	1.0	1.0	9148.0	6.0
08	9156.0	0.0	0.0	0.0
09	0.0	4981.0	0.0	4175.0
10	35.0	0.0	9121.0	0.0
11	26.0	0.0	0.0	9130.0
12	1.0	9154.0	0.0	1.0
13	9150.0	0.0	6.0	0.0
14	0.0	117.0	756.0	8283.0
15	1691.0	5731.0	740.0	994.0
16	1333.5	4710.5	379.5	2732.5
17	2481.75	1794.75	1683.75	3195.75

PFM

	A	C	G	T
01	0.293	0.187	0.231	0.288
02	0.363	0.142	0.131	0.364
03	0.256	0.019	0.6	0.124
04	0.105	0.015	0.783	0.097
05	0.687	0.275	0.038	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.999	0.001
08	1.0	0.0	0.0	0.0
09	0.0	0.544	0.0	0.456
10	0.004	0.0	0.996	0.0
11	0.003	0.0	0.0	0.997
12	0.0	1.0	0.0	0.0
13	0.999	0.0	0.001	0.0
14	0.0	0.013	0.083	0.905
15	0.185	0.626	0.081	0.109
16	0.146	0.514	0.041	0.298
17	0.271	0.196	0.184	0.349

PWM

	A	C	G	T
01	0.159	-0.288	-0.078	0.143
02	0.373	-0.568	-0.642	0.375
03	0.025	-2.559	0.875	-0.697
04	-0.867	-2.8	1.141	-0.946
05	1.01	0.096	-1.89	-6.073
06	-6.549	-6.912	-6.283	1.385
07	-6.549	-6.549	1.385	-5.623
08	1.386	-6.912	-6.912	-6.912
09	-6.912	0.777	-6.912	0.601
10	-4.118	-6.912	1.382	-6.912
11	-4.395	-6.912	-6.912	1.383
12	-6.549	1.385	-6.912	-6.549
13	1.385	-6.912	-5.623	-6.912
14	-6.912	-2.955	-1.106	1.285
15	-0.302	0.917	-1.127	-0.833
16	-0.54	0.721	-1.792	0.177
17	0.081	-0.243	-0.307	0.333

Standard thresholds

P-value	Threshold
0.001	-5.22009
0.0005	-3.09159
0.0001	1.80531