TBXT.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TBXT.H12INVIVO.1.PSM.A
Gene (human)	TBXT (GeneCards)
Gene synonyms (human)	T
Gene (mouse)	Tbxt
Gene synonyms (mouse)	T
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	14
Consensus	ndRSGTGYGAdddn
GC content	46.84%
Information content (bits; total / per base)	11.845 / 0.846
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9873

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)	0.772	0.805	0.637	0.681	0.769	0.809	2.275	2.488	56.591	89.796
Mouse	6 (36)	0.733	0.832	0.613	0.714	0.718	0.808	2.14	2.682	92.956	205.097

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.982	0.971	0.97	0.954	0.945	0.924
Overall, 6 experiments	best	0.999	0.998	0.997	0.995	0.992	0.988
Methyl HT-SELEX, 2 experiments	median	0.986	0.976	0.976	0.963	0.958	0.941
Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.996	0.993	0.99	0.985
Non-Methyl HT-SELEX, 4 experiments	median	0.975	0.967	0.893	0.889	0.819	0.821
Non-Methyl HT-SELEX, 4 experiments	best	0.999	0.998	0.997	0.995	0.992	0.988

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.H12INVIVO.1.PSM.A.pcm
PWM	TBXT.H12INVIVO.1.PSM.A.pwm
PFM	TBXT.H12INVIVO.1.PSM.A.pfm
Alignment	TBXT.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	TBXT.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	TBXT.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	TBXT.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	TBXT.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	TBXT.H12INVIVO.1.PSM.A_homer_format_0.001.txt TBXT.H12INVIVO.1.PSM.A_homer_format_0.0005.txt TBXT.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2012.5	2560.5	3528.5	1771.5
02	2037.25	1382.25	2757.25	3696.25
03	6909.0	280.0	2152.0	532.0
04	768.0	912.0	7423.0	770.0
05	450.0	59.0	9306.0	58.0
06	1.0	274.0	0.0	9598.0
07	0.0	1.0	9872.0	0.0
08	332.0	2676.0	47.0	6818.0
09	72.0	407.0	7888.0	1506.0
10	9747.0	14.0	80.0	32.0
11	5490.0	954.0	1638.0	1791.0
12	4120.0	1136.0	2059.0	2558.0
13	1916.0	1107.0	1568.0	5282.0
14	1833.0	2303.0	2360.0	3377.0

PFM

	A	C	G	T
01	0.204	0.259	0.357	0.179
02	0.206	0.14	0.279	0.374
03	0.7	0.028	0.218	0.054
04	0.078	0.092	0.752	0.078
05	0.046	0.006	0.943	0.006
06	0.0	0.028	0.0	0.972
07	0.0	0.0	1.0	0.0
08	0.034	0.271	0.005	0.691
09	0.007	0.041	0.799	0.153
10	0.987	0.001	0.008	0.003
11	0.556	0.097	0.166	0.181
12	0.417	0.115	0.209	0.259
13	0.194	0.112	0.159	0.535
14	0.186	0.233	0.239	0.342

PWM

	A	C	G	T
01	-0.204	0.037	0.357	-0.331
02	-0.192	-0.579	0.111	0.404
03	1.029	-2.169	-0.137	-1.531
04	-1.165	-0.994	1.1	-1.163
05	-1.698	-3.696	1.326	-3.713
06	-6.618	-2.191	-6.98	1.357
07	-6.98	-6.618	1.385	-6.98
08	-2.0	0.081	-3.914	1.015
09	-3.504	-1.798	1.161	-0.493
10	1.373	-5.021	-3.402	-4.277
11	0.799	-0.949	-0.41	-0.32
12	0.512	-0.775	-0.181	0.036
13	-0.253	-0.801	-0.453	0.76
14	-0.297	-0.069	-0.045	0.313

Standard thresholds

P-value	Threshold
0.001	4.09901
0.0005	5.22631
0.0001	7.35786