SIX1.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX1.H12RSNP.0.P.B
Gene (human)	SIX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Six1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	14
Consensus	KGWAAYhKGAYMYb
GC content	39.95%
Information content (bits; total / per base)	12.668 / 0.905
Data sources	ChIP-Seq
Aligned words	145

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)	0.928	0.942	0.873	0.901	0.924	0.943	4.101	4.672	262.77	331.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.72	0.691	0.651	0.63	0.59	0.587
Overall, 4 experiments	best	0.87	0.847	0.733	0.723	0.645	0.642
Methyl HT-SELEX, 2 experiments	median	0.72	0.696	0.64	0.627	0.58	0.581
Methyl HT-SELEX, 2 experiments	best	0.87	0.847	0.732	0.723	0.632	0.64
Non-Methyl HT-SELEX, 2 experiments	median	0.72	0.691	0.651	0.63	0.597	0.588
Non-Methyl HT-SELEX, 2 experiments	best	0.85	0.825	0.733	0.715	0.645	0.642

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.729	0.47	0.788	0.625

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.0.P.B.pcm
PWM	SIX1.H12RSNP.0.P.B.pwm
PFM	SIX1.H12RSNP.0.P.B.pfm
Alignment	SIX1.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	SIX1.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	SIX1.H12RSNP.0.P.B_jaspar_format.txt
MEME format	SIX1.H12RSNP.0.P.B_meme_format.meme
Transfac format	SIX1.H12RSNP.0.P.B_transfac_format.txt
Homer format	SIX1.H12RSNP.0.P.B_homer_format_0.001.txt SIX1.H12RSNP.0.P.B_homer_format_0.0005.txt SIX1.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	26.0	2.0	30.0	87.0
02	2.0	2.0	139.0	2.0
03	53.0	5.0	4.0	83.0
04	133.0	4.0	1.0	7.0
05	140.0	1.0	2.0	2.0
06	4.0	89.0	8.0	44.0
07	32.0	59.0	10.0	44.0
08	8.0	11.0	20.0	106.0
09	18.0	2.0	123.0	2.0
10	142.0	0.0	1.0	2.0
11	6.0	29.0	27.0	83.0
12	72.0	65.0	6.0	2.0
13	12.0	69.0	6.0	58.0
14	13.0	62.0	34.0	36.0

PFM

	A	C	G	T
01	0.179	0.014	0.207	0.6
02	0.014	0.014	0.959	0.014
03	0.366	0.034	0.028	0.572
04	0.917	0.028	0.007	0.048
05	0.966	0.007	0.014	0.014
06	0.028	0.614	0.055	0.303
07	0.221	0.407	0.069	0.303
08	0.055	0.076	0.138	0.731
09	0.124	0.014	0.848	0.014
10	0.979	0.0	0.007	0.014
11	0.041	0.2	0.186	0.572
12	0.497	0.448	0.041	0.014
13	0.083	0.476	0.041	0.4
14	0.09	0.428	0.234	0.248

PWM

	A	C	G	T
01	-0.319	-2.447	-0.182	0.856
02	-2.447	-2.447	1.319	-2.447
03	0.369	-1.793	-1.967	0.81
04	1.275	-1.967	-2.816	-1.515
05	1.326	-2.816	-2.447	-2.447
06	-1.967	0.878	-1.4	0.188
07	-0.12	0.474	-1.204	0.188
08	-1.4	-1.119	-0.568	1.051
09	-0.667	-2.447	1.198	-2.447
10	1.34	-3.406	-2.816	-2.447
11	-1.644	-0.215	-0.283	0.81
12	0.67	0.569	-1.644	-2.447
13	-1.041	0.628	-1.644	0.457
14	-0.968	0.523	-0.062	-0.007

Standard thresholds

P-value	Threshold
0.001	4.23191
0.0005	5.17826
0.0001	7.14796