ATF4.H12INVIVO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ATF4.H12INVIVO.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	nnRKMTGACGTCAThhn
GC content	45.99%
Information content (bits; total / per base)	19.184 / 1.128
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2469

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)	0.811	0.851	0.6	0.679	0.688	0.733	1.639	1.843	73.955	150.721
Mouse	2 (9)	0.747	0.772	0.556	0.571	0.642	0.663	1.585	1.628	49.357	62.125

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.776	0.766	0.623	0.642	0.553	0.579
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	0.998	0.915	0.918
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.999	0.998	0.915	0.918
Non-Methyl HT-SELEX, 5 experiments	median	0.641	0.611	0.568	0.563	0.534	0.538
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
#	3.299	3.166	0.212	0.177

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.H12INVIVO.2.SM.B.pcm
PWM	ATF4.H12INVIVO.2.SM.B.pwm
PFM	ATF4.H12INVIVO.2.SM.B.pfm
Alignment	ATF4.H12INVIVO.2.SM.B.words.tsv
Threshold to P-value map	ATF4.H12INVIVO.2.SM.B.thr
Motif in other formats
JASPAR format	ATF4.H12INVIVO.2.SM.B_jaspar_format.txt
MEME format	ATF4.H12INVIVO.2.SM.B_meme_format.meme
Transfac format	ATF4.H12INVIVO.2.SM.B_transfac_format.txt
Homer format	ATF4.H12INVIVO.2.SM.B_homer_format_0.001.txt ATF4.H12INVIVO.2.SM.B_homer_format_0.0005.txt ATF4.H12INVIVO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	684.75	505.75	582.75	695.75
02	911.5	361.5	361.5	834.5
03	599.0	84.0	1362.0	424.0
04	185.0	63.0	1954.0	267.0
05	1549.0	808.0	109.0	3.0
06	8.0	8.0	6.0	2447.0
07	6.0	7.0	2453.0	3.0
08	2468.0	1.0	0.0	0.0
09	0.0	1782.0	0.0	687.0
10	6.0	0.0	2463.0	0.0
11	14.0	6.0	1.0	2448.0
12	10.0	2450.0	3.0	6.0
13	2456.0	2.0	6.0	5.0
14	13.0	17.0	201.0	2238.0
15	489.0	1342.0	237.0	401.0
16	561.75	979.75	161.75	765.75
17	588.0	547.0	438.0	896.0

PFM

	A	C	G	T
01	0.277	0.205	0.236	0.282
02	0.369	0.146	0.146	0.338
03	0.243	0.034	0.552	0.172
04	0.075	0.026	0.791	0.108
05	0.627	0.327	0.044	0.001
06	0.003	0.003	0.002	0.991
07	0.002	0.003	0.994	0.001
08	1.0	0.0	0.0	0.0
09	0.0	0.722	0.0	0.278
10	0.002	0.0	0.998	0.0
11	0.006	0.002	0.0	0.991
12	0.004	0.992	0.001	0.002
13	0.995	0.001	0.002	0.002
14	0.005	0.007	0.081	0.906
15	0.198	0.544	0.096	0.162
16	0.228	0.397	0.066	0.31
17	0.238	0.222	0.177	0.363

PWM

	A	C	G	T
01	0.103	-0.199	-0.057	0.119
02	0.389	-0.533	-0.533	0.301
03	-0.03	-1.975	0.79	-0.374
04	-1.198	-2.255	1.15	-0.834
05	0.918	0.269	-1.719	-4.828
06	-4.131	-4.131	-4.355	1.375
07	-4.355	-4.236	1.377	-4.828
08	1.384	-5.346	-5.759	-5.759
09	-5.759	1.058	-5.759	0.107
10	-4.355	-5.759	1.381	-5.759
11	-3.659	-4.355	-5.346	1.375
12	-3.947	1.376	-4.828	-4.355
13	1.379	-5.054	-4.355	-4.489
14	-3.724	-3.486	-1.115	1.286
15	-0.232	0.775	-0.952	-0.43
16	-0.094	0.461	-1.33	0.215
17	-0.048	-0.12	-0.342	0.372

Standard thresholds

P-value	Threshold
0.001	-1.68619
0.0005	0.05226
0.0001	3.80686