TBX2.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TBX2.H12INVITRO.0.SM.B
Gene (human)	TBX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Tbx2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	ndAGGTGTbRn
GC content	47.51%
Information content (bits; total / per base)	10.417 / 0.947
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9870

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.847	0.809	0.81	0.746	0.767	0.709
Overall, 5 experiments	best	0.943	0.909	0.913	0.873	0.866	0.824
Methyl HT-SELEX, 2 experiments	median	0.895	0.847	0.862	0.809	0.816	0.766
Methyl HT-SELEX, 2 experiments	best	0.943	0.909	0.913	0.873	0.866	0.824
Non-Methyl HT-SELEX, 3 experiments	median	0.843	0.809	0.728	0.707	0.635	0.634
Non-Methyl HT-SELEX, 3 experiments	best	0.881	0.818	0.848	0.785	0.801	0.745

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.993	0.406	0.97	0.67
batch 2	0.625	0.211	0.669	0.471

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: 6.5.4.0.1
HGNC	HGNC:11597
MGI	MGI:98494
EntrezGene (human)	GeneID:6909 (SSTAR profile)
EntrezGene (mouse)	GeneID:21385 (SSTAR profile)
UniProt ID (human)	TBX2_HUMAN
UniProt ID (mouse)	TBX2_MOUSE
UniProt AC (human)	Q13207 (TFClass)
UniProt AC (mouse)	Q60707 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	2

PCM	TBX2.H12INVITRO.0.SM.B.pcm
PWM	TBX2.H12INVITRO.0.SM.B.pwm
PFM	TBX2.H12INVITRO.0.SM.B.pfm
Alignment	TBX2.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	TBX2.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	TBX2.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	TBX2.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	TBX2.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	TBX2.H12INVITRO.0.SM.B_homer_format_0.001.txt TBX2.H12INVITRO.0.SM.B_homer_format_0.0005.txt TBX2.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3131.5	1604.5	2604.5	2529.5
02	4044.0	1043.0	2669.0	2114.0
03	8102.0	200.0	1106.0	462.0
04	315.0	337.0	9076.0	142.0
05	7.0	8.0	9854.0	1.0
06	8.0	245.0	13.0	9604.0
07	14.0	3.0	9844.0	9.0
08	796.0	429.0	199.0	8446.0
09	570.0	2180.0	3658.0	3462.0
10	5947.75	873.75	1727.75	1320.75
11	3752.5	1804.5	2099.5	2213.5

PFM

	A	C	G	T
01	0.317	0.163	0.264	0.256
02	0.41	0.106	0.27	0.214
03	0.821	0.02	0.112	0.047
04	0.032	0.034	0.92	0.014
05	0.001	0.001	0.998	0.0
06	0.001	0.025	0.001	0.973
07	0.001	0.0	0.997	0.001
08	0.081	0.043	0.02	0.856
09	0.058	0.221	0.371	0.351
10	0.603	0.089	0.175	0.134
11	0.38	0.183	0.213	0.224

PWM

	A	C	G	T
01	0.238	-0.43	0.054	0.025
02	0.494	-0.86	0.078	-0.154
03	1.188	-2.502	-0.801	-1.671
04	-2.052	-1.985	1.302	-2.84
05	-5.582	-5.48	1.384	-6.618
06	-5.48	-2.301	-5.084	1.358
07	-5.021	-6.144	1.383	-5.387
08	-1.129	-1.745	-2.507	1.23
09	-1.462	-0.124	0.393	0.338
10	0.879	-1.036	-0.356	-0.624
11	0.419	-0.313	-0.161	-0.109

Standard thresholds

P-value	Threshold
0.001	4.680175
0.0005	5.619625
0.0001	7.56398