GBX2.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GBX2.H12RSNP.0.SM.B
Gene (human)	GBX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Gbx2
Gene synonyms (mouse)	Mmoxa, Stra7
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	14
Consensus	nhSYTAATTRvnbn
GC content	40.68%
Information content (bits; total / per base)	12.555 / 0.897
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2450

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.896	0.861	0.775	0.758	0.655	0.665
Overall, 10 experiments	best	0.989	0.981	0.982	0.971	0.971	0.956
Methyl HT-SELEX, 2 experiments	median	0.96	0.938	0.911	0.89	0.832	0.825
Methyl HT-SELEX, 2 experiments	best	0.987	0.977	0.978	0.965	0.959	0.942
Non-Methyl HT-SELEX, 8 experiments	median	0.787	0.756	0.661	0.655	0.582	0.594
Non-Methyl HT-SELEX, 8 experiments	best	0.989	0.981	0.982	0.971	0.971	0.956

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.972	0.602	0.94	0.508
batch 2	0.854	0.793	0.866	0.63

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.H12RSNP.0.SM.B.pcm
PWM	GBX2.H12RSNP.0.SM.B.pwm
PFM	GBX2.H12RSNP.0.SM.B.pfm
Alignment	GBX2.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	GBX2.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	GBX2.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	GBX2.H12RSNP.0.SM.B_meme_format.meme
Transfac format	GBX2.H12RSNP.0.SM.B_transfac_format.txt
Homer format	GBX2.H12RSNP.0.SM.B_homer_format_0.001.txt GBX2.H12RSNP.0.SM.B_homer_format_0.0005.txt GBX2.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	597.5	595.5	650.5	606.5
02	476.5	1137.5	391.5	444.5
03	566.0	604.0	1242.0	38.0
04	40.0	1775.0	222.0	413.0
05	0.0	10.0	0.0	2440.0
06	2450.0	0.0	0.0	0.0
07	2450.0	0.0	0.0	0.0
08	0.0	0.0	0.0	2450.0
09	1.0	62.0	25.0	2362.0
10	1354.0	0.0	1091.0	5.0
11	395.0	1046.0	884.0	125.0
12	303.0	751.0	748.0	648.0
13	382.25	949.25	615.25	503.25
14	637.5	591.5	561.5	659.5

PFM

	A	C	G	T
01	0.244	0.243	0.266	0.248
02	0.194	0.464	0.16	0.181
03	0.231	0.247	0.507	0.016
04	0.016	0.724	0.091	0.169
05	0.0	0.004	0.0	0.996
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	0.025	0.01	0.964
10	0.553	0.0	0.445	0.002
11	0.161	0.427	0.361	0.051
12	0.124	0.307	0.305	0.264
13	0.156	0.387	0.251	0.205
14	0.26	0.241	0.229	0.269

PWM

	A	C	G	T
01	-0.025	-0.028	0.06	-0.01
02	-0.25	0.618	-0.446	-0.319
03	-0.079	-0.014	0.705	-2.733
04	-2.684	1.062	-1.009	-0.393
05	-5.752	-3.94	-5.752	1.38
06	1.384	-5.752	-5.752	-5.752
07	1.384	-5.752	-5.752	-5.752
08	-5.752	-5.752	-5.752	1.384
09	-5.339	-2.263	-3.127	1.347
10	0.792	-5.752	0.576	-4.482
11	-0.437	0.534	0.366	-1.577
12	-0.701	0.203	0.199	0.056
13	-0.47	0.437	0.004	-0.196
14	0.04	-0.035	-0.087	0.074

Standard thresholds

P-value	Threshold
0.001	2.75991
0.0005	4.33791
0.0001	7.64986