SIX1.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX1.H12RSNP.1.SM.B
Gene (human)	SIX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Six1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	9
Consensus	nYGATACbn
GC content	45.94%
Information content (bits; total / per base)	9.836 / 1.093
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9843

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	3 (18)	0.595	0.648	0.43	0.458	0.558	0.592	1.255	1.392	26.525	42.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.931	0.893	0.889	0.847	0.801	0.771
Overall, 4 experiments	best	0.937	0.905	0.901	0.86	0.829	0.794
Methyl HT-SELEX, 2 experiments	median	0.916	0.871	0.862	0.817	0.77	0.741
Methyl HT-SELEX, 2 experiments	best	0.927	0.884	0.882	0.837	0.792	0.762
Non-Methyl HT-SELEX, 2 experiments	median	0.936	0.904	0.899	0.859	0.819	0.787
Non-Methyl HT-SELEX, 2 experiments	best	0.937	0.905	0.901	0.86	0.829	0.794

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.725	0.436	0.789	0.589

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HD-SINE {3.1.6} (TFClass)
TF subfamily	SIX1-like {3.1.6.1} (TFClass)
TFClass ID	TFClass: 3.1.6.1.1
HGNC	HGNC:10887
MGI	MGI:102780
EntrezGene (human)	GeneID:6495 (SSTAR profile)
EntrezGene (mouse)	GeneID:20471 (SSTAR profile)
UniProt ID (human)	SIX1_HUMAN
UniProt ID (mouse)	SIX1_MOUSE
UniProt AC (human)	Q15475 (TFClass)
UniProt AC (mouse)	Q62231 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	SIX1.H12RSNP.1.SM.B.pcm
PWM	SIX1.H12RSNP.1.SM.B.pwm
PFM	SIX1.H12RSNP.1.SM.B.pfm
Alignment	SIX1.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	SIX1.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	SIX1.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	SIX1.H12RSNP.1.SM.B_meme_format.meme
Transfac format	SIX1.H12RSNP.1.SM.B_transfac_format.txt
Homer format	SIX1.H12RSNP.1.SM.B_homer_format_0.001.txt SIX1.H12RSNP.1.SM.B_homer_format_0.0005.txt SIX1.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2411.0	2262.0	2942.0	2228.0
02	250.0	2676.0	720.0	6197.0
03	22.0	3.0	9814.0	4.0
04	9827.0	0.0	0.0	16.0
05	2.0	55.0	1.0	9785.0
06	9538.0	305.0	0.0	0.0
07	43.0	7826.0	429.0	1545.0
08	704.5	3811.5	4321.5	1005.5
09	1459.5	2742.5	2788.5	2852.5

PFM

	A	C	G	T
01	0.245	0.23	0.299	0.226
02	0.025	0.272	0.073	0.63
03	0.002	0.0	0.997	0.0
04	0.998	0.0	0.0	0.002
05	0.0	0.006	0.0	0.994
06	0.969	0.031	0.0	0.0
07	0.004	0.795	0.044	0.157
08	0.072	0.387	0.439	0.102
09	0.148	0.279	0.283	0.29

PWM

	A	C	G	T
01	-0.02	-0.084	0.178	-0.099
02	-2.279	0.084	-1.227	0.923
03	-4.619	-6.142	1.383	-5.969
04	1.384	-6.977	-6.977	-4.902
05	-6.351	-3.761	-6.616	1.38
06	1.354	-2.081	-6.977	-6.977
07	-3.996	1.156	-1.742	-0.465
08	-1.248	0.437	0.563	-0.894
09	-0.522	0.108	0.125	0.148

Standard thresholds

P-value	Threshold
0.001	5.026935
0.0005	6.044065
0.0001	7.621805