SIX2.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H12RSNP.0.P.B
Gene (human)	SIX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Six2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	14
Consensus	WGWAAYhWRAbMYb
GC content	38.89%
Information content (bits; total / per base)	12.089 / 0.864
Data sources	ChIP-Seq
Aligned words	1000

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	5 (34)	0.904	0.929	0.814	0.864	0.914	0.936	3.53	3.961	248.168	300.569
Mouse	8 (52)	0.892	0.928	0.812	0.866	0.892	0.929	3.364	3.829	211.571	334.174

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.686	0.659	0.629	0.61	0.58	0.574
Overall, 4 experiments	best	0.872	0.834	0.77	0.74	0.667	0.661
Methyl HT-SELEX, 2 experiments	median	0.704	0.679	0.648	0.628	0.592	0.586
Methyl HT-SELEX, 2 experiments	best	0.872	0.834	0.77	0.74	0.667	0.661
Non-Methyl HT-SELEX, 2 experiments	median	0.683	0.656	0.627	0.609	0.578	0.572
Non-Methyl HT-SELEX, 2 experiments	best	0.836	0.793	0.733	0.704	0.643	0.635

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	27.273	3.862	0.443	0.36

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.767	0.509	0.812	0.635

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: 3.1.6.1.2
HGNC	HGNC:10888
MGI	MGI:102778
EntrezGene (human)	GeneID:10736 (SSTAR profile)
EntrezGene (mouse)	GeneID:20472 (SSTAR profile)
UniProt ID (human)	SIX2_HUMAN
UniProt ID (mouse)	SIX2_MOUSE
UniProt AC (human)	Q9NPC8 (TFClass)
UniProt AC (mouse)	Q62232 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 8 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	SIX2.H12RSNP.0.P.B.pcm
PWM	SIX2.H12RSNP.0.P.B.pwm
PFM	SIX2.H12RSNP.0.P.B.pfm
Alignment	SIX2.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	SIX2.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	SIX2.H12RSNP.0.P.B_jaspar_format.txt
MEME format	SIX2.H12RSNP.0.P.B_meme_format.meme
Transfac format	SIX2.H12RSNP.0.P.B_transfac_format.txt
Homer format	SIX2.H12RSNP.0.P.B_homer_format_0.001.txt SIX2.H12RSNP.0.P.B_homer_format_0.0005.txt SIX2.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	215.0	11.0	196.0	578.0
02	12.0	4.0	982.0	2.0
03	515.0	37.0	42.0	406.0
04	898.0	59.0	9.0	34.0
05	992.0	2.0	5.0	1.0
06	41.0	532.0	64.0	363.0
07	238.0	409.0	63.0	290.0
08	130.0	90.0	97.0	683.0
09	177.0	15.0	766.0	42.0
10	991.0	2.0	3.0	4.0
11	79.0	174.0	251.0	496.0
12	517.0	425.0	21.0	37.0
13	87.0	558.0	48.0	307.0
14	139.0	367.0	212.0	282.0

PFM

	A	C	G	T
01	0.215	0.011	0.196	0.578
02	0.012	0.004	0.982	0.002
03	0.515	0.037	0.042	0.406
04	0.898	0.059	0.009	0.034
05	0.992	0.002	0.005	0.001
06	0.041	0.532	0.064	0.363
07	0.238	0.409	0.063	0.29
08	0.13	0.09	0.097	0.683
09	0.177	0.015	0.766	0.042
10	0.991	0.002	0.003	0.004
11	0.079	0.174	0.251	0.496
12	0.517	0.425	0.021	0.037
13	0.087	0.558	0.048	0.307
14	0.139	0.367	0.212	0.282

PWM

	A	C	G	T
01	-0.15	-2.985	-0.241	0.834
02	-2.909	-3.783	1.363	-4.213
03	0.719	-1.872	-1.75	0.482
04	1.274	-1.422	-3.156	-1.952
05	1.373	-4.213	-3.622	-4.525
06	-1.774	0.752	-1.343	0.371
07	-0.049	0.49	-1.358	0.147
08	-0.648	-1.01	-0.936	1.001
09	-0.342	-2.711	1.115	-1.75
10	1.372	-4.213	-3.975	-3.783
11	-1.137	-0.359	0.004	0.682
12	0.723	0.528	-2.405	-1.872
13	-1.043	0.799	-1.622	0.204
14	-0.582	0.382	-0.164	0.12

Standard thresholds

P-value	Threshold
0.001	4.09281
0.0005	5.14861
0.0001	7.26411