SIX1.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX1.H12INVITRO.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	10
Consensus	ndbGATAYSn
GC content	45.51%
Information content (bits; total / per base)	8.997 / 0.9
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9464

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)	0.574	0.607	0.404	0.431	0.532	0.559	1.174	1.329	15.921	23.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.931	0.893	0.889	0.846	0.806	0.774
Overall, 4 experiments	best	0.947	0.92	0.904	0.868	0.825	0.795
Methyl HT-SELEX, 2 experiments	median	0.918	0.876	0.864	0.82	0.77	0.743
Methyl HT-SELEX, 2 experiments	best	0.928	0.888	0.88	0.837	0.789	0.761
Non-Methyl HT-SELEX, 2 experiments	median	0.941	0.909	0.9	0.861	0.824	0.791
Non-Methyl HT-SELEX, 2 experiments	best	0.947	0.92	0.904	0.868	0.825	0.795

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.674	0.362	0.697	0.526

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.H12INVITRO.1.SM.B.pcm
PWM	SIX1.H12INVITRO.1.SM.B.pwm
PFM	SIX1.H12INVITRO.1.SM.B.pfm
Alignment	SIX1.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	SIX1.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	SIX1.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	SIX1.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	SIX1.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	SIX1.H12INVITRO.1.SM.B_homer_format_0.001.txt SIX1.H12INVITRO.1.SM.B_homer_format_0.0005.txt SIX1.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2890.25	2484.25	1867.25	2222.25
02	4223.5	1073.5	2709.5	1457.5
03	535.0	3710.0	909.0	4310.0
04	186.0	200.0	9077.0	1.0
05	9079.0	75.0	15.0	295.0
06	122.0	0.0	4.0	9338.0
07	9098.0	320.0	37.0	9.0
08	346.0	7281.0	800.0	1037.0
09	720.25	2914.25	5118.25	711.25
10	2094.0	2263.0	2215.0	2892.0

PFM

	A	C	G	T
01	0.305	0.262	0.197	0.235
02	0.446	0.113	0.286	0.154
03	0.057	0.392	0.096	0.455
04	0.02	0.021	0.959	0.0
05	0.959	0.008	0.002	0.031
06	0.013	0.0	0.0	0.987
07	0.961	0.034	0.004	0.001
08	0.037	0.769	0.085	0.11
09	0.076	0.308	0.541	0.075
10	0.221	0.239	0.234	0.306

PWM

	A	C	G	T
01	0.2	0.049	-0.236	-0.063
02	0.579	-0.789	0.135	-0.484
03	-1.483	0.449	-0.955	0.599
04	-2.532	-2.46	1.344	-6.579
05	1.344	-3.422	-4.92	-2.075
06	-2.947	-6.942	-5.931	1.372
07	1.346	-1.994	-4.099	-5.346
08	-1.917	1.123	-1.082	-0.824
09	-1.187	0.208	0.771	-1.2
10	-0.122	-0.044	-0.066	0.201

Standard thresholds

P-value	Threshold
0.001	5.084535
0.0005	5.976475
0.0001	7.55119