ATF4.H12INVITRO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ATF4.H12INVITRO.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	16
Consensus	ndRdMTGACGTCAKMn
GC content	50.67%
Information content (bits; total / per base)	17.984 / 1.124
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	6163

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)	0.737	0.768	0.513	0.558	0.639	0.697	1.401	1.621	26.772	46.444
Mouse	2 (9)	0.685	0.728	0.482	0.546	0.618	0.664	1.439	1.561	25.481	36.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.777	0.769	0.623	0.644	0.555	0.581
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.996	0.995	0.859	0.875
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.996	0.995	0.859	0.875
Non-Methyl HT-SELEX, 5 experiments	median	0.64	0.616	0.567	0.565	0.535	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
#	3.046	2.879	0.132	0.116

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.H12INVITRO.2.SM.B.pcm
PWM	ATF4.H12INVITRO.2.SM.B.pwm
PFM	ATF4.H12INVITRO.2.SM.B.pfm
Alignment	ATF4.H12INVITRO.2.SM.B.words.tsv
Threshold to P-value map	ATF4.H12INVITRO.2.SM.B.thr
Motif in other formats
JASPAR format	ATF4.H12INVITRO.2.SM.B_jaspar_format.txt
MEME format	ATF4.H12INVITRO.2.SM.B_meme_format.meme
Transfac format	ATF4.H12INVITRO.2.SM.B_transfac_format.txt
Homer format	ATF4.H12INVITRO.2.SM.B_homer_format_0.001.txt ATF4.H12INVITRO.2.SM.B_homer_format_0.0005.txt ATF4.H12INVITRO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1720.0	1083.0	1774.0	1586.0
02	1854.5	923.5	1057.5	2327.5
03	1249.0	181.0	4228.0	505.0
04	938.0	501.0	3300.0	1424.0
05	4634.0	773.0	719.0	37.0
06	17.0	15.0	67.0	6064.0
07	23.0	1.0	6116.0	23.0
08	6130.0	3.0	24.0	6.0
09	12.0	6075.0	23.0	53.0
10	19.0	0.0	6140.0	4.0
11	17.0	73.0	73.0	6000.0
12	171.0	5818.0	102.0	72.0
13	5918.0	44.0	130.0	71.0
14	58.0	398.0	2477.0	3230.0
15	816.0	4023.0	685.0	639.0
16	1244.75	2158.75	979.75	1779.75

PFM

	A	C	G	T
01	0.279	0.176	0.288	0.257
02	0.301	0.15	0.172	0.378
03	0.203	0.029	0.686	0.082
04	0.152	0.081	0.535	0.231
05	0.752	0.125	0.117	0.006
06	0.003	0.002	0.011	0.984
07	0.004	0.0	0.992	0.004
08	0.995	0.0	0.004	0.001
09	0.002	0.986	0.004	0.009
10	0.003	0.0	0.996	0.001
11	0.003	0.012	0.012	0.974
12	0.028	0.944	0.017	0.012
13	0.96	0.007	0.021	0.012
14	0.009	0.065	0.402	0.524
15	0.132	0.653	0.111	0.104
16	0.202	0.35	0.159	0.289

PWM

	A	C	G	T
01	0.11	-0.352	0.141	0.029
02	0.185	-0.511	-0.376	0.412
03	-0.21	-2.131	1.009	-1.113
04	-0.495	-1.12	0.761	-0.079
05	1.1	-0.688	-0.761	-3.673
06	-4.387	-4.498	-3.105	1.369
07	-4.115	-6.184	1.378	-4.115
08	1.38	-5.696	-4.076	-5.24
09	-4.689	1.371	-4.115	-3.331
10	-4.288	-6.561	1.381	-5.52
11	-4.387	-3.022	-3.022	1.358
12	-2.187	1.328	-2.695	-3.035
13	1.345	-3.509	-2.457	-3.048
14	-3.244	-1.35	0.474	0.739
15	-0.634	0.959	-0.809	-0.878
16	-0.213	0.337	-0.452	0.144

Standard thresholds

P-value	Threshold
0.001	0.10301
0.0005	1.66146
0.0001	4.94516