TBXT.H12RSNP.1.PSM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TBXT.H12RSNP.1.PSM.D
Gene (human)	TBXT (GeneCards)
Gene synonyms (human)	T
Gene (mouse)	Tbxt
Gene synonyms (mouse)	T
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	12
Consensus	nRbGTGYKAddd
GC content	44.49%
Information content (bits; total / per base)	10.118 / 0.843
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9117

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	2 (14)	0.758	0.793	0.626	0.667	0.761	0.804	2.246	2.467	55.513	97.222
Mouse	6 (36)	0.725	0.831	0.606	0.722	0.715	0.808	2.17	2.823	90.206	205.229

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.983	0.972	0.972	0.957	0.949	0.928
Overall, 6 experiments	best	0.999	0.998	0.997	0.996	0.993	0.99
Methyl HT-SELEX, 2 experiments	median	0.987	0.978	0.978	0.966	0.962	0.946
Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.996	0.994	0.991	0.988
Non-Methyl HT-SELEX, 4 experiments	median	0.976	0.969	0.895	0.891	0.817	0.822
Non-Methyl HT-SELEX, 4 experiments	best	0.999	0.998	0.997	0.996	0.993	0.99

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	T-Box factors {6.5} (TFClass)
TF family	Brachyury-related {6.5.1} (TFClass)
TF subfamily	{6.5.1.0} (TFClass)
TFClass ID	TFClass: 6.5.1.0.1
HGNC	HGNC:11515
MGI	MGI:98472
EntrezGene (human)	GeneID:6862 (SSTAR profile)
EntrezGene (mouse)	GeneID:20997 (SSTAR profile)
UniProt ID (human)	TBXT_HUMAN
UniProt ID (mouse)	TBXT_MOUSE
UniProt AC (human)	O15178 (TFClass)
UniProt AC (mouse)	P20293 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 6 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	TBXT.H12RSNP.1.PSM.D.pcm
PWM	TBXT.H12RSNP.1.PSM.D.pwm
PFM	TBXT.H12RSNP.1.PSM.D.pfm
Alignment	TBXT.H12RSNP.1.PSM.D.words.tsv
Threshold to P-value map	TBXT.H12RSNP.1.PSM.D.thr
Motif in other formats
JASPAR format	TBXT.H12RSNP.1.PSM.D_jaspar_format.txt
MEME format	TBXT.H12RSNP.1.PSM.D_meme_format.meme
Transfac format	TBXT.H12RSNP.1.PSM.D_transfac_format.txt
Homer format	TBXT.H12RSNP.1.PSM.D_homer_format_0.001.txt TBXT.H12RSNP.1.PSM.D_homer_format_0.0005.txt TBXT.H12RSNP.1.PSM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2400.75	1507.75	2136.75	3071.75
02	5773.5	393.5	1780.5	1169.5
03	970.0	1751.0	5328.0	1068.0
04	1089.0	39.0	7931.0	58.0
05	0.0	1091.0	0.0	8026.0
06	0.0	0.0	9117.0	0.0
07	417.0	2022.0	14.0	6664.0
08	78.0	519.0	6587.0	1933.0
09	8956.0	6.0	151.0	4.0
10	4851.0	1178.0	1323.0	1765.0
11	4052.75	1329.75	1754.75	1979.75
12	2384.0	1257.0	1461.0	4015.0

PFM

	A	C	G	T
01	0.263	0.165	0.234	0.337
02	0.633	0.043	0.195	0.128
03	0.106	0.192	0.584	0.117
04	0.119	0.004	0.87	0.006
05	0.0	0.12	0.0	0.88
06	0.0	0.0	1.0	0.0
07	0.046	0.222	0.002	0.731
08	0.009	0.057	0.722	0.212
09	0.982	0.001	0.017	0.0
10	0.532	0.129	0.145	0.194
11	0.445	0.146	0.192	0.217
12	0.261	0.138	0.16	0.44

PWM

	A	C	G	T
01	0.052	-0.413	-0.064	0.298
02	0.929	-1.752	-0.247	-0.666
03	-0.853	-0.263	0.849	-0.757
04	-0.737	-4.012	1.246	-3.634
05	-6.909	-0.736	-6.909	1.258
06	-6.909	-6.909	1.386	-6.909
07	-1.694	-0.12	-4.943	1.072
08	-3.347	-1.476	1.061	-0.165
09	1.368	-5.619	-2.7	-5.895
10	0.755	-0.659	-0.543	-0.255
11	0.575	-0.538	-0.261	-0.141
12	0.045	-0.594	-0.444	0.566

Standard thresholds

P-value	Threshold
0.001	4.88776
0.0005	5.785565
0.0001	7.424145