TBX3.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TBX3.H12INVIVO.0.PSM.A
Gene (human)	TBX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Tbx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	ndAGGTGTSAdd
GC content	52.21%
Information content (bits; total / per base)	12.425 / 1.035
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9672

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)	0.698	0.701	0.536	0.543	0.658	0.668	1.715	1.817	50.081	62.301
Mouse	3 (17)	0.671	0.706	0.483	0.554	0.638	0.658	1.532	1.675	11.432	39.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.966	0.944	0.946	0.919	0.905	0.874
Overall, 2 experiments	best	0.983	0.971	0.968	0.952	0.932	0.91
Methyl HT-SELEX, 1 experiments	median	0.983	0.971	0.968	0.952	0.932	0.91
Methyl HT-SELEX, 1 experiments	best	0.983	0.971	0.968	0.952	0.932	0.91
Non-Methyl HT-SELEX, 1 experiments	median	0.949	0.917	0.924	0.887	0.877	0.838
Non-Methyl HT-SELEX, 1 experiments	best	0.949	0.917	0.924	0.887	0.877	0.838

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	12.201	2.767	0.049	0.024

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.943	0.485	0.88	0.606
batch 2	0.787	0.64	0.827	0.6

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	T-Box factors {6.5} (TFClass)
TF family	TBX2-related {6.5.4} (TFClass)
TF subfamily	{6.5.4.0} (TFClass)
TFClass ID	TFClass: 6.5.4.0.2
HGNC	HGNC:11602
MGI	MGI:98495
EntrezGene (human)	GeneID:6926 (SSTAR profile)
EntrezGene (mouse)	GeneID:21386 (SSTAR profile)
UniProt ID (human)	TBX3_HUMAN
UniProt ID (mouse)	TBX3_MOUSE
UniProt AC (human)	O15119 (TFClass)
UniProt AC (mouse)	P70324 (TFClass)
GRECO-DB-TF	yes

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

PCM	TBX3.H12INVIVO.0.PSM.A.pcm
PWM	TBX3.H12INVIVO.0.PSM.A.pwm
PFM	TBX3.H12INVIVO.0.PSM.A.pfm
Alignment	TBX3.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	TBX3.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	TBX3.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	TBX3.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	TBX3.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	TBX3.H12INVIVO.0.PSM.A_homer_format_0.001.txt TBX3.H12INVIVO.0.PSM.A_homer_format_0.0005.txt TBX3.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1787.5	1692.5	3542.5	2649.5
02	3390.75	652.75	3696.75	1931.75
03	8590.0	22.0	894.0	166.0
04	29.0	191.0	9451.0	1.0
05	0.0	0.0	9672.0	0.0
06	0.0	909.0	0.0	8763.0
07	0.0	0.0	9672.0	0.0
08	236.0	449.0	18.0	8969.0
09	130.0	2142.0	5333.0	2067.0
10	7478.0	59.0	1899.0	236.0
11	3635.25	1600.25	2828.25	1608.25
12	2147.0	1443.0	4433.0	1649.0

PFM

	A	C	G	T
01	0.185	0.175	0.366	0.274
02	0.351	0.067	0.382	0.2
03	0.888	0.002	0.092	0.017
04	0.003	0.02	0.977	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.094	0.0	0.906
07	0.0	0.0	1.0	0.0
08	0.024	0.046	0.002	0.927
09	0.013	0.221	0.551	0.214
10	0.773	0.006	0.196	0.024
11	0.376	0.165	0.292	0.166
12	0.222	0.149	0.458	0.17

PWM

	A	C	G	T
01	-0.302	-0.356	0.382	0.091
02	0.338	-1.307	0.424	-0.224
03	1.267	-4.601	-0.993	-2.666
04	-4.348	-2.527	1.362	-6.599
05	-6.961	-6.961	1.386	-6.961
06	-6.961	-0.977	-6.961	1.287
07	-6.961	-6.961	1.386	-6.961
08	-2.318	-1.68	-4.781	1.31
09	-2.907	-0.121	0.79	-0.157
10	1.128	-3.676	-0.241	-2.318
11	0.407	-0.412	0.157	-0.407
12	-0.119	-0.516	0.606	-0.382

Standard thresholds

P-value	Threshold
0.001	3.47486
0.0005	4.855145
0.0001	7.35382