TBX3.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TBX3.H12INVITRO.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	11
Consensus	ndAGGTGTbRn
GC content	50.95%
Information content (bits; total / per base)	11.291 / 1.026
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	2495

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)	0.675	0.684	0.526	0.529	0.648	0.653	1.674	1.76	48.921	58.921
Mouse	3 (17)	0.648	0.705	0.464	0.542	0.618	0.657	1.452	1.667	10.187	36.481

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.97	0.95	0.946	0.92	0.89	0.863
Overall, 2 experiments	best	0.985	0.975	0.966	0.951	0.913	0.893
Methyl HT-SELEX, 1 experiments	median	0.985	0.975	0.966	0.951	0.913	0.893
Methyl HT-SELEX, 1 experiments	best	0.985	0.975	0.966	0.951	0.913	0.893
Non-Methyl HT-SELEX, 1 experiments	median	0.954	0.925	0.925	0.89	0.868	0.833
Non-Methyl HT-SELEX, 1 experiments	best	0.954	0.925	0.925	0.89	0.868	0.833

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.693	1.934	0.046	0.024

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.929	0.491	0.866	0.668
batch 2	0.782	0.636	0.791	0.572

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.H12INVITRO.0.PSM.A.pcm
PWM	TBX3.H12INVITRO.0.PSM.A.pwm
PFM	TBX3.H12INVITRO.0.PSM.A.pfm
Alignment	TBX3.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	TBX3.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	TBX3.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	TBX3.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	TBX3.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	TBX3.H12INVITRO.0.PSM.A_homer_format_0.001.txt TBX3.H12INVITRO.0.PSM.A_homer_format_0.0005.txt TBX3.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	505.5	542.5	755.5	691.5
02	965.0	209.0	850.0	471.0
03	2251.0	7.0	206.0	31.0
04	1.0	29.0	2465.0	0.0
05	0.0	0.0	2495.0	0.0
06	1.0	48.0	0.0	2446.0
07	0.0	0.0	2494.0	1.0
08	220.0	138.0	58.0	2079.0
09	108.0	663.0	924.0	800.0
10	1482.75	127.75	638.75	245.75
11	614.5	625.5	707.5	547.5

PFM

	A	C	G	T
01	0.203	0.217	0.303	0.277
02	0.387	0.084	0.341	0.189
03	0.902	0.003	0.083	0.012
04	0.0	0.012	0.988	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.019	0.0	0.98
07	0.0	0.0	1.0	0.0
08	0.088	0.055	0.023	0.833
09	0.043	0.266	0.37	0.321
10	0.594	0.051	0.256	0.098
11	0.246	0.251	0.284	0.219

PWM

	A	C	G	T
01	-0.209	-0.139	0.191	0.103
02	0.435	-1.087	0.309	-0.28
03	1.281	-4.247	-1.102	-2.944
04	-5.355	-3.006	1.372	-5.768
05	-5.768	-5.768	1.384	-5.768
06	-5.355	-2.528	-5.768	1.364
07	-5.768	-5.768	1.384	-5.355
08	-1.036	-1.498	-2.345	1.202
09	-1.739	0.061	0.392	0.248
10	0.864	-1.574	0.024	-0.927
11	-0.015	0.003	0.126	-0.13

Standard thresholds

P-value	Threshold
0.001	4.24236
0.0005	5.4052
0.0001	7.538075