GSX2.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GSX2.H12RSNP.0.SM.B
Gene (human)	GSX2 (GeneCards)
Gene synonyms (human)	GSH2
Gene (mouse)	Gsx2
Gene synonyms (mouse)	Gsh-2, Gsh2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	13
Consensus	nndYTAATKAvnn
GC content	32.59%
Information content (bits; total / per base)	11.346 / 0.873
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2495

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.927	0.88	0.892	0.845	0.817	0.783
Overall, 4 experiments	best	0.937	0.894	0.924	0.877	0.88	0.836
Methyl HT-SELEX, 1 experiments	median	0.93	0.883	0.916	0.866	0.872	0.825
Methyl HT-SELEX, 1 experiments	best	0.93	0.883	0.916	0.866	0.872	0.825
Non-Methyl HT-SELEX, 3 experiments	median	0.923	0.877	0.869	0.824	0.763	0.741
Non-Methyl HT-SELEX, 3 experiments	best	0.937	0.894	0.924	0.877	0.88	0.836

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.737	0.544	0.682	0.488

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	GSX {3.1.1.12} (TFClass)
TFClass ID	TFClass: 3.1.1.12.2
HGNC	HGNC:24959
MGI	MGI:95843
EntrezGene (human)	GeneID:170825 (SSTAR profile)
EntrezGene (mouse)	GeneID:14843 (SSTAR profile)
UniProt ID (human)	GSX2_HUMAN
UniProt ID (mouse)	GSX2_MOUSE
UniProt AC (human)	Q9BZM3 (TFClass)
UniProt AC (mouse)	P31316 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	GSX2.H12RSNP.0.SM.B.pcm
PWM	GSX2.H12RSNP.0.SM.B.pwm
PFM	GSX2.H12RSNP.0.SM.B.pfm
Alignment	GSX2.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	GSX2.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	GSX2.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	GSX2.H12RSNP.0.SM.B_meme_format.meme
Transfac format	GSX2.H12RSNP.0.SM.B_transfac_format.txt
Homer format	GSX2.H12RSNP.0.SM.B_homer_format_0.001.txt GSX2.H12RSNP.0.SM.B_homer_format_0.0005.txt GSX2.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	486.75	671.75	587.75	748.75
02	627.5	844.5	534.5	488.5
03	1215.0	305.0	639.0	336.0
04	47.0	855.0	78.0	1515.0
05	3.0	0.0	0.0	2492.0
06	2491.0	4.0	0.0	0.0
07	2495.0	0.0	0.0	0.0
08	1.0	8.0	0.0	2486.0
09	18.0	28.0	799.0	1650.0
10	1951.0	29.0	486.0	29.0
11	299.0	721.0	1179.0	296.0
12	368.25	783.25	691.25	652.25
13	619.75	643.75	681.75	549.75

PFM

	A	C	G	T
01	0.195	0.269	0.236	0.3
02	0.252	0.338	0.214	0.196
03	0.487	0.122	0.256	0.135
04	0.019	0.343	0.031	0.607
05	0.001	0.0	0.0	0.999
06	0.998	0.002	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.003	0.0	0.996
09	0.007	0.011	0.32	0.661
10	0.782	0.012	0.195	0.012
11	0.12	0.289	0.473	0.119
12	0.148	0.314	0.277	0.261
13	0.248	0.258	0.273	0.22

PWM

	A	C	G	T
01	-0.247	0.074	-0.059	0.182
02	0.006	0.302	-0.154	-0.244
03	0.665	-0.712	0.024	-0.616
04	-2.548	0.315	-2.057	0.886
05	-4.838	-5.768	-5.768	1.383
06	1.382	-4.655	-5.768	-5.768
07	1.384	-5.768	-5.768	-5.768
08	-5.355	-4.141	-5.768	1.38
09	-3.445	-3.039	0.247	0.971
10	1.138	-3.006	-0.249	-3.006
11	-0.732	0.144	0.635	-0.742
12	-0.525	0.227	0.102	0.045
13	-0.006	0.031	0.089	-0.126

Standard thresholds

P-value	Threshold
0.001	3.86321
0.0005	5.36726
0.0001	7.829165