SIX1.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX1.H12INVIVO.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	13
Consensus	nhhnYGATACSnn
GC content	49.04%
Information content (bits; total / per base)	10.85 / 0.835
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2496

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)	0.664	0.707	0.499	0.556	0.631	0.662	1.578	1.755	46.317	64.041

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.928	0.883	0.891	0.845	0.81	0.775
Overall, 4 experiments	best	0.935	0.898	0.904	0.861	0.834	0.797
Methyl HT-SELEX, 2 experiments	median	0.916	0.867	0.867	0.82	0.778	0.747
Methyl HT-SELEX, 2 experiments	best	0.933	0.896	0.892	0.849	0.806	0.775
Non-Methyl HT-SELEX, 2 experiments	median	0.929	0.884	0.897	0.85	0.824	0.786
Non-Methyl HT-SELEX, 2 experiments	best	0.935	0.898	0.904	0.861	0.834	0.797

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.727	0.417	0.73	0.53

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.H12INVIVO.1.SM.B.pcm
PWM	SIX1.H12INVIVO.1.SM.B.pwm
PFM	SIX1.H12INVIVO.1.SM.B.pfm
Alignment	SIX1.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	SIX1.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	SIX1.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	SIX1.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	SIX1.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	SIX1.H12INVIVO.1.SM.B_homer_format_0.001.txt SIX1.H12INVIVO.1.SM.B_homer_format_0.0005.txt SIX1.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	893.25	673.25	395.25	534.25
02	1060.25	600.25	327.25	508.25
03	528.0	1204.0	279.0	485.0
04	564.0	716.0	800.0	416.0
05	14.0	1172.0	109.0	1201.0
06	2.0	1.0	2491.0	2.0
07	2482.0	0.0	0.0	14.0
08	6.0	23.0	1.0	2466.0
09	2461.0	35.0	0.0	0.0
10	1.0	2191.0	39.0	265.0
11	140.0	1190.0	1006.0	160.0
12	383.25	945.25	510.25	657.25
13	562.25	638.25	565.25	730.25

PFM

	A	C	G	T
01	0.358	0.27	0.158	0.214
02	0.425	0.24	0.131	0.204
03	0.212	0.482	0.112	0.194
04	0.226	0.287	0.321	0.167
05	0.006	0.47	0.044	0.481
06	0.001	0.0	0.998	0.001
07	0.994	0.0	0.0	0.006
08	0.002	0.009	0.0	0.988
09	0.986	0.014	0.0	0.0
10	0.0	0.878	0.016	0.106
11	0.056	0.477	0.403	0.064
12	0.154	0.379	0.204	0.263
13	0.225	0.256	0.226	0.293

PWM

	A	C	G	T
01	0.358	0.076	-0.455	-0.155
02	0.529	-0.039	-0.643	-0.204
03	-0.166	0.656	-0.801	-0.251
04	-0.101	0.137	0.248	-0.404
05	-3.669	0.629	-1.73	0.653
06	-5.064	-5.356	1.382	-5.064
07	1.378	-5.769	-5.769	-3.669
08	-4.365	-3.222	-5.356	1.372
09	1.37	-2.83	-5.769	-5.769
10	-5.356	1.254	-2.727	-0.852
11	-1.484	0.644	0.476	-1.352
12	-0.486	0.414	-0.201	0.052
13	-0.104	0.023	-0.099	0.157

Standard thresholds

P-value	Threshold
0.001	4.30691
0.0005	5.65846
0.0001	7.79267