GSX1.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GSX1.H12INVITRO.0.SM.B
Gene (human)	GSX1 (GeneCards)
Gene synonyms (human)	GSH1
Gene (mouse)	Gsx1
Gene synonyms (mouse)	Gsh-1, Gsh1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	nvYTAATGAbn
GC content	36.88%
Information content (bits; total / per base)	11.201 / 1.018
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	5710

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.817	0.769	0.762	0.728	0.711	0.687
Overall, 4 experiments	best	0.97	0.947	0.955	0.928	0.904	0.877
Methyl HT-SELEX, 1 experiments	median	0.931	0.884	0.908	0.859	0.862	0.815
Methyl HT-SELEX, 1 experiments	best	0.931	0.884	0.908	0.859	0.862	0.815
Non-Methyl HT-SELEX, 3 experiments	median	0.704	0.653	0.616	0.597	0.56	0.56
Non-Methyl HT-SELEX, 3 experiments	best	0.97	0.947	0.955	0.928	0.904	0.877

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.582	0.35	0.494	0.359

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: 3.1.1.12.1
HGNC	HGNC:20374
MGI	MGI:95842
EntrezGene (human)	GeneID:219409 (SSTAR profile)
EntrezGene (mouse)	GeneID:14842 (SSTAR profile)
UniProt ID (human)	GSX1_HUMAN
UniProt ID (mouse)	GSX1_MOUSE
UniProt AC (human)	Q9H4S2 (TFClass)
UniProt AC (mouse)	P31315 (TFClass)
GRECO-DB-TF	yes

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

PCM	GSX1.H12INVITRO.0.SM.B.pcm
PWM	GSX1.H12INVITRO.0.SM.B.pwm
PFM	GSX1.H12INVITRO.0.SM.B.pfm
Alignment	GSX1.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	GSX1.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	GSX1.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	GSX1.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	GSX1.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	GSX1.H12INVITRO.0.SM.B_homer_format_0.001.txt GSX1.H12INVITRO.0.SM.B_homer_format_0.0005.txt GSX1.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1419.25	1864.25	1186.25	1240.25
02	1730.75	1147.75	2152.75	678.75
03	302.0	1701.0	429.0	3278.0
04	0.0	0.0	0.0	5710.0
05	5710.0	0.0	0.0	0.0
06	5710.0	0.0	0.0	0.0
07	0.0	2419.0	0.0	3291.0
08	0.0	0.0	4672.0	1038.0
09	5608.0	0.0	102.0	0.0
10	290.25	1482.25	2905.25	1032.25
11	1296.75	1630.75	1474.75	1307.75

PFM

	A	C	G	T
01	0.249	0.326	0.208	0.217
02	0.303	0.201	0.377	0.119
03	0.053	0.298	0.075	0.574
04	0.0	0.0	0.0	1.0
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.424	0.0	0.576
08	0.0	0.0	0.818	0.182
09	0.982	0.0	0.018	0.0
10	0.051	0.26	0.509	0.181
11	0.227	0.286	0.258	0.229

PWM

	A	C	G	T
01	-0.006	0.267	-0.185	-0.14
02	0.192	-0.218	0.41	-0.742
03	-1.548	0.175	-1.199	0.83
04	-6.494	-6.494	-6.494	1.385
05	1.385	-6.494	-6.494	-6.494
06	1.385	-6.494	-6.494	-6.494
07	-6.494	0.527	-6.494	0.834
08	-6.494	-6.494	1.185	-0.318
09	1.367	-6.494	-2.619	-6.494
10	-1.587	0.038	0.71	-0.324
11	-0.096	0.133	0.033	-0.087

Standard thresholds

P-value	Threshold
0.001	3.743105
0.0005	5.782335
0.0001	7.88015