GSX2.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GSX2.H12INVITRO.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	12
Consensus	nvvYTAATTRvn
GC content	36.06%
Information content (bits; total / per base)	11.128 / 0.927
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8821

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.943	0.911	0.909	0.871	0.838	0.806
Overall, 4 experiments	best	0.964	0.937	0.956	0.925	0.932	0.899
Methyl HT-SELEX, 1 experiments	median	0.947	0.914	0.926	0.887	0.88	0.841
Methyl HT-SELEX, 1 experiments	best	0.947	0.914	0.926	0.887	0.88	0.841
Non-Methyl HT-SELEX, 3 experiments	median	0.939	0.907	0.892	0.854	0.796	0.772
Non-Methyl HT-SELEX, 3 experiments	best	0.964	0.937	0.956	0.925	0.932	0.899

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.732	0.507	0.665	0.44

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.H12INVITRO.0.SM.B.pcm
PWM	GSX2.H12INVITRO.0.SM.B.pwm
PFM	GSX2.H12INVITRO.0.SM.B.pfm
Alignment	GSX2.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	GSX2.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	GSX2.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	GSX2.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	GSX2.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	GSX2.H12INVITRO.0.SM.B_homer_format_0.001.txt GSX2.H12INVITRO.0.SM.B_homer_format_0.0005.txt GSX2.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2122.75	2195.75	2375.75	2126.75
02	1652.0	3803.0	1795.0	1571.0
03	2633.0	2204.0	3463.0	521.0
04	47.0	5137.0	429.0	3208.0
05	0.0	0.0	0.0	8821.0
06	8821.0	0.0	0.0	0.0
07	8821.0	0.0	0.0	0.0
08	0.0	0.0	0.0	8821.0
09	77.0	92.0	1956.0	6696.0
10	4885.0	55.0	3711.0	170.0
11	1566.25	3136.25	2805.25	1313.25
12	1757.25	2507.25	2501.25	2055.25

PFM

	A	C	G	T
01	0.241	0.249	0.269	0.241
02	0.187	0.431	0.203	0.178
03	0.298	0.25	0.393	0.059
04	0.005	0.582	0.049	0.364
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	0.009	0.01	0.222	0.759
10	0.554	0.006	0.421	0.019
11	0.178	0.356	0.318	0.149
12	0.199	0.284	0.284	0.233

PWM

	A	C	G	T
01	-0.038	-0.004	0.074	-0.036
02	-0.289	0.545	-0.206	-0.339
03	0.177	-0.001	0.451	-1.44
04	-3.802	0.845	-1.633	0.374
05	-6.879	-6.879	-6.879	1.386
06	1.386	-6.879	-6.879	-6.879
07	1.386	-6.879	-6.879	-6.879
08	-6.879	-6.879	-6.879	1.386
09	-3.327	-3.153	-0.12	1.11
10	0.795	-3.652	0.52	-2.551
11	-0.342	0.352	0.24	-0.518
12	-0.227	0.128	0.126	-0.07

Standard thresholds

P-value	Threshold
0.001	3.844265
0.0005	5.556485
0.0001	7.944885