EOMES.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	EOMES.H12RSNP.0.PSM.A
Gene (human)	EOMES (GeneCards)
Gene synonyms (human)	TBR2
Gene (mouse)	Eomes
Gene synonyms (mouse)	Tbr2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	ndAGGTGTGAWh
GC content	43.07%
Information content (bits; total / per base)	15.136 / 1.261
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9990

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	4 (24)	0.757	0.803	0.619	0.675	0.738	0.791	2.181	2.458	82.726	182.108
Mouse	4 (20)	0.826	0.882	0.733	0.796	0.794	0.846	2.578	2.76	117.471	183.569

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.98	0.967	0.956	0.938	0.886	0.875
Overall, 4 experiments	best	0.998	0.997	0.989	0.985	0.933	0.913
Methyl HT-SELEX, 1 experiments	median	0.986	0.977	0.97	0.955	0.933	0.913
Methyl HT-SELEX, 1 experiments	best	0.986	0.977	0.97	0.955	0.933	0.913
Non-Methyl HT-SELEX, 3 experiments	median	0.974	0.958	0.943	0.92	0.88	0.854
Non-Methyl HT-SELEX, 3 experiments	best	0.998	0.997	0.989	0.985	0.893	0.896

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.622	0.043	0.477	0.327

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	T-Box factors {6.5} (TFClass)
TF family	TBrain-related {6.5.2} (TFClass)
TF subfamily	{6.5.2.0} (TFClass)
TFClass ID	TFClass: 6.5.2.0.2
HGNC	HGNC:3372
MGI	MGI:1201683
EntrezGene (human)	GeneID:8320 (SSTAR profile)
EntrezGene (mouse)	GeneID:13813 (SSTAR profile)
UniProt ID (human)	EOMES_HUMAN
UniProt ID (mouse)	EOMES_MOUSE
UniProt AC (human)	O95936 (TFClass)
UniProt AC (mouse)	O54839 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	4 human, 4 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	EOMES.H12RSNP.0.PSM.A.pcm
PWM	EOMES.H12RSNP.0.PSM.A.pwm
PFM	EOMES.H12RSNP.0.PSM.A.pfm
Alignment	EOMES.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	EOMES.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	EOMES.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	EOMES.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	EOMES.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	EOMES.H12RSNP.0.PSM.A_homer_format_0.001.txt EOMES.H12RSNP.0.PSM.A_homer_format_0.0005.txt EOMES.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3595.25	1840.25	2117.25	2437.25
02	4571.5	563.5	2331.5	2523.5
03	9471.0	19.0	428.0	72.0
04	170.0	46.0	9745.0	29.0
05	0.0	1.0	9989.0	0.0
06	0.0	54.0	7.0	9929.0
07	0.0	0.0	9990.0	0.0
08	70.0	755.0	3.0	9162.0
09	26.0	143.0	8745.0	1076.0
10	9907.0	11.0	29.0	43.0
11	5777.75	937.75	822.75	2451.75
12	4338.25	1642.25	1410.25	2599.25

PFM

	A	C	G	T
01	0.36	0.184	0.212	0.244
02	0.458	0.056	0.233	0.253
03	0.948	0.002	0.043	0.007
04	0.017	0.005	0.975	0.003
05	0.0	0.0	1.0	0.0
06	0.0	0.005	0.001	0.994
07	0.0	0.0	1.0	0.0
08	0.007	0.076	0.0	0.917
09	0.003	0.014	0.875	0.108
10	0.992	0.001	0.003	0.004
11	0.578	0.094	0.082	0.245
12	0.434	0.164	0.141	0.26

PWM

	A	C	G	T
01	0.364	-0.305	-0.165	-0.024
02	0.604	-1.486	-0.069	0.01
03	1.332	-4.765	-1.759	-3.516
04	-2.675	-3.946	1.361	-4.38
05	-6.99	-6.629	1.386	-6.99
06	-6.99	-3.793	-5.594	1.379
07	-6.99	-6.99	1.386	-6.99
08	-3.543	-1.194	-6.156	1.299
09	-4.481	-2.845	1.253	-0.841
10	1.377	-5.236	-4.38	-4.011
11	0.838	-0.978	-1.109	-0.018
12	0.552	-0.419	-0.571	0.04

Standard thresholds

P-value	Threshold
0.001	1.171315
0.0005	2.800315
0.0001	6.059815