GBX2.H12INVIVO.1.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GBX2.H12INVIVO.1.S.D
Gene (human)	GBX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Gbx2
Gene synonyms (mouse)	Mmoxa, Stra7
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	20
Consensus	nvSTAATTASbvnhWWWWdn
GC content	31.23%
Information content (bits; total / per base)	15.455 / 0.773
Data sources	HT-SELEX
Aligned words	9258

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.907	0.886	0.766	0.761	0.642	0.661
Overall, 10 experiments	best	0.997	0.996	0.981	0.977	0.96	0.938
Methyl HT-SELEX, 2 experiments	median	0.962	0.945	0.902	0.886	0.817	0.814
Methyl HT-SELEX, 2 experiments	best	0.983	0.971	0.973	0.957	0.949	0.929
Non-Methyl HT-SELEX, 8 experiments	median	0.79	0.767	0.656	0.657	0.579	0.594
Non-Methyl HT-SELEX, 8 experiments	best	0.997	0.996	0.981	0.977	0.96	0.938

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.902	0.147	0.901	0.491
batch 2	0.809	0.726	0.786	0.532

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.1.S.D.pcm
PWM	GBX2.H12INVIVO.1.S.D.pwm
PFM	GBX2.H12INVIVO.1.S.D.pfm
Alignment	GBX2.H12INVIVO.1.S.D.words.tsv
Threshold to P-value map	GBX2.H12INVIVO.1.S.D.thr
Motif in other formats
JASPAR format	GBX2.H12INVIVO.1.S.D_jaspar_format.txt
MEME format	GBX2.H12INVIVO.1.S.D_meme_format.meme
Transfac format	GBX2.H12INVIVO.1.S.D_transfac_format.txt
Homer format	GBX2.H12INVIVO.1.S.D_homer_format_0.001.txt GBX2.H12INVIVO.1.S.D_homer_format_0.0005.txt GBX2.H12INVIVO.1.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2393.5	3475.5	1818.5	1570.5
02	3244.5	2806.5	2374.5	832.5
03	314.0	6459.0	1580.0	905.0
04	0.0	1299.0	0.0	7959.0
05	9258.0	0.0	0.0	0.0
06	9258.0	0.0	0.0	0.0
07	0.0	0.0	0.0	9258.0
08	0.0	0.0	0.0	9258.0
09	6530.0	0.0	2728.0	0.0
10	892.0	2297.0	5873.0	196.0
11	776.0	3191.0	1580.0	3711.0
12	1643.0	3582.0	2508.0	1525.0
13	3033.0	2789.0	1241.0	2195.0
14	3483.0	1677.0	833.0	3265.0
15	4291.0	952.0	321.0	3694.0
16	4997.0	378.0	92.0	3791.0
17	4444.0	122.0	182.0	4510.0
18	3154.0	306.0	666.0	5132.0
19	2712.25	610.25	1993.25	3942.25
20	2301.75	1351.75	2732.75	2871.75

PFM

	A	C	G	T
01	0.259	0.375	0.196	0.17
02	0.35	0.303	0.256	0.09
03	0.034	0.698	0.171	0.098
04	0.0	0.14	0.0	0.86
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.705	0.0	0.295	0.0
10	0.096	0.248	0.634	0.021
11	0.084	0.345	0.171	0.401
12	0.177	0.387	0.271	0.165
13	0.328	0.301	0.134	0.237
14	0.376	0.181	0.09	0.353
15	0.463	0.103	0.035	0.399
16	0.54	0.041	0.01	0.409
17	0.48	0.013	0.02	0.487
18	0.341	0.033	0.072	0.554
19	0.293	0.066	0.215	0.426
20	0.249	0.146	0.295	0.31

PWM

	A	C	G	T
01	0.034	0.406	-0.241	-0.387
02	0.337	0.193	0.026	-1.021
03	-1.991	1.026	-0.381	-0.937
04	-6.922	-0.577	-6.922	1.234
05	1.386	-6.922	-6.922	-6.922
06	1.386	-6.922	-6.922	-6.922
07	-6.922	-6.922	-6.922	1.386
08	-6.922	-6.922	-6.922	1.386
09	1.037	-6.922	0.164	-6.922
10	-0.952	-0.008	0.931	-2.458
11	-1.091	0.321	-0.381	0.472
12	-0.342	0.436	0.08	-0.417
13	0.27	0.186	-0.622	-0.053
14	0.408	-0.322	-1.02	0.344
15	0.617	-0.887	-1.969	0.467
16	0.769	-1.807	-3.202	0.493
17	0.652	-2.925	-2.531	0.667
18	0.309	-2.017	-1.243	0.796
19	0.158	-1.33	-0.149	0.532
20	-0.006	-0.537	0.166	0.216

Standard thresholds

P-value	Threshold
0.001	0.25991
0.0005	2.16461
0.0001	6.23026