GMEB1.H13RSNP.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GMEB1.H13RSNP.2.SM.B
Gene (human)	GMEB1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Gmeb1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	16
Consensus	nbTACGTMAbbnvvnn
GC content	47.23%
Information content (bits; total / per base)	12.279 / 0.767
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8330
Previous names	GMEB1.H12RSNP.2.SM.B

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	1 (7)	0.816	0.841	0.694	0.719	0.687	0.711	1.952	2.067	37.745	55.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.824	0.795	0.793	0.766	0.741	0.72
Overall, 2 experiments	best	0.985	0.977	0.961	0.946	0.891	0.874
Methyl HT-SELEX, 1 experiments	median	0.662	0.613	0.625	0.586	0.592	0.566
Methyl HT-SELEX, 1 experiments	best	0.662	0.613	0.625	0.586	0.592	0.566
Non-Methyl HT-SELEX, 1 experiments	median	0.985	0.977	0.961	0.946	0.891	0.874
Non-Methyl HT-SELEX, 1 experiments	best	0.985	0.977	0.961	0.946	0.891	0.874

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.726	0.155	0.459	0.333

TF superclass	alpha-Helices exposed by beta-structures {5} (TFClass)
TF class	SAND domain factors {5.3} (TFClass)
TF family	GMEB {5.3.3} (TFClass)
TF subfamily	GMEB {5.3.3.1} (TFClass)
TFClass ID	TFClass: 5.3.3.1.1
HGNC	HGNC:4370
MGI	MGI:2135604
EntrezGene (human)	GeneID:10691 (SSTAR profile)
EntrezGene (mouse)	GeneID:56809 (SSTAR profile)
UniProt ID (human)	GMEB1_HUMAN
UniProt ID (mouse)	GMEB1_MOUSE
UniProt AC (human)	Q9Y692 (TFClass)
UniProt AC (mouse)	Q9JL60 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	GMEB1.H13RSNP.2.SM.B.pcm
PWM	GMEB1.H13RSNP.2.SM.B.pwm
PFM	GMEB1.H13RSNP.2.SM.B.pfm
Threshold to P-value map	GMEB1.H13RSNP.2.SM.B.thr
Motif in other formats
JASPAR format	GMEB1.H13RSNP.2.SM.B_jaspar_format.txt
MEME format	GMEB1.H13RSNP.2.SM.B_meme_format.meme
Transfac format	GMEB1.H13RSNP.2.SM.B_transfac_format.txt
Homer format	GMEB1.H13RSNP.2.SM.B_homer_format_0.001.txt GMEB1.H13RSNP.2.SM.B_homer_format_0.0005.txt GMEB1.H13RSNP.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1668.25	2818.25	1768.25	2075.25
02	674.0	1024.0	1814.0	4818.0
03	271.0	333.0	1019.0	6707.0
04	6721.0	0.0	1609.0	0.0
05	0.0	8330.0	0.0	0.0
06	0.0	0.0	8330.0	0.0
07	0.0	4.0	0.0	8326.0
08	6028.0	1956.0	346.0	0.0
09	8156.0	109.0	62.0	3.0
10	774.0	2299.0	2691.0	2566.0
11	575.0	2439.0	3342.0	1974.0
12	2896.0	1640.0	1288.0	2506.0
13	1957.0	3436.0	1530.0	1407.0
14	1347.0	2340.0	3543.0	1100.0
15	967.25	2418.25	2553.25	2391.25
16	2174.0	1969.0	1936.0	2251.0

PFM

	A	C	G	T
01	0.2	0.338	0.212	0.249
02	0.081	0.123	0.218	0.578
03	0.033	0.04	0.122	0.805
04	0.807	0.0	0.193	0.0
05	0.0	1.0	0.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	0.0	1.0
08	0.724	0.235	0.042	0.0
09	0.979	0.013	0.007	0.0
10	0.093	0.276	0.323	0.308
11	0.069	0.293	0.401	0.237
12	0.348	0.197	0.155	0.301
13	0.235	0.412	0.184	0.169
14	0.162	0.281	0.425	0.132
15	0.116	0.29	0.307	0.287
16	0.261	0.236	0.232	0.27

PWM

	A	C	G	T
01	-0.222	0.302	-0.163	-0.003
02	-1.126	-0.709	-0.138	0.838
03	-2.032	-1.828	-0.714	1.169
04	1.171	-6.828	-0.258	-6.828
05	-6.828	1.385	-6.828	-6.828
06	-6.828	-6.828	1.385	-6.828
07	-6.828	-5.809	-6.828	1.385
08	1.062	-0.063	-1.789	-6.828
09	1.364	-2.931	-3.48	-5.983
10	-0.988	0.099	0.256	0.209
11	-1.284	0.158	0.473	-0.053
12	0.329	-0.239	-0.48	0.185
13	-0.062	0.5	-0.308	-0.392
14	-0.435	0.116	0.531	-0.637
15	-0.766	0.149	0.204	0.138
16	0.043	-0.056	-0.073	0.078

Standard thresholds

P-value	Threshold
0.001	3.43811
0.0005	5.02376
0.0001	7.52111