GBX2.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GBX2.H12INVIVO.0.SM.D
Gene (human)	GBX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Gbx2
Gene synonyms (mouse)	Mmoxa, Stra7
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nvvbTAATTRvn
GC content	37.45%
Information content (bits; total / per base)	11.9 / 0.992
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8831

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.906	0.873	0.782	0.767	0.657	0.67
Overall, 10 experiments	best	0.992	0.986	0.983	0.973	0.97	0.956
Methyl HT-SELEX, 2 experiments	median	0.962	0.942	0.914	0.894	0.833	0.827
Methyl HT-SELEX, 2 experiments	best	0.988	0.98	0.979	0.967	0.96	0.943
Non-Methyl HT-SELEX, 8 experiments	median	0.802	0.77	0.671	0.665	0.587	0.599
Non-Methyl HT-SELEX, 8 experiments	best	0.992	0.986	0.983	0.973	0.97	0.956

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.956	0.545	0.924	0.525
batch 2	0.865	0.814	0.863	0.609

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	GBX {3.1.1.11} (TFClass)
TFClass ID	TFClass: 3.1.1.11.2
HGNC	HGNC:4186
MGI	MGI:95668
EntrezGene (human)	GeneID:2637 (SSTAR profile)
EntrezGene (mouse)	GeneID:14472 (SSTAR profile)
UniProt ID (human)	GBX2_HUMAN
UniProt ID (mouse)	GBX2_MOUSE
UniProt AC (human)	P52951 (TFClass)
UniProt AC (mouse)	P48031 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	8
Methyl-HT-SELEX	2

PCM	GBX2.H12INVIVO.0.SM.D.pcm
PWM	GBX2.H12INVIVO.0.SM.D.pwm
PFM	GBX2.H12INVIVO.0.SM.D.pfm
Alignment	GBX2.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	GBX2.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	GBX2.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	GBX2.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	GBX2.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	GBX2.H12INVIVO.0.SM.D_homer_format_0.001.txt GBX2.H12INVIVO.0.SM.D_homer_format_0.0005.txt GBX2.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2236.25	2058.25	2433.25	2103.25
02	1620.0	3692.0	2149.0	1370.0
03	1985.0	2376.0	4120.0	350.0
04	341.0	4695.0	1397.0	2398.0
05	0.0	0.0	0.0	8831.0
06	8831.0	0.0	0.0	0.0
07	8831.0	0.0	0.0	0.0
08	0.0	0.0	0.0	8831.0
09	1.0	56.0	89.0	8685.0
10	3908.0	0.0	4864.0	59.0
11	1069.75	3470.75	3307.75	982.75
12	1389.0	2504.0	2475.0	2463.0

PFM

	A	C	G	T
01	0.253	0.233	0.276	0.238
02	0.183	0.418	0.243	0.155
03	0.225	0.269	0.467	0.04
04	0.039	0.532	0.158	0.272
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.006	0.01	0.983
10	0.443	0.0	0.551	0.007
11	0.121	0.393	0.375	0.111
12	0.157	0.284	0.28	0.279

PWM

	A	C	G	T
01	0.013	-0.07	0.097	-0.048
02	-0.309	0.514	-0.027	-0.477
03	-0.106	0.073	0.623	-1.836
04	-1.862	0.754	-0.457	0.083
05	-6.88	-6.88	-6.88	1.386
06	1.386	-6.88	-6.88	-6.88
07	1.386	-6.88	-6.88	-6.88
08	-6.88	-6.88	-6.88	1.386
09	-6.516	-3.636	-3.187	1.369
10	0.571	-6.88	0.789	-3.585
11	-0.723	0.452	0.404	-0.808
12	-0.463	0.126	0.114	0.109

Standard thresholds

P-value	Threshold
0.001	2.401275
0.0005	4.41542
0.0001	8.00025