SIX2.H13RSNP.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H13RSNP.2.SM.B
Gene (human)	SIX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Six2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	9
Consensus	nYGATACvn
GC content	50.36%
Information content (bits; total / per base)	8.833 / 0.981
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2437
Previous names	SIX2.H12RSNP.2.SM.B

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)	0.625	0.655	0.44	0.476	0.576	0.598	1.256	1.325	28.184	38.602
Mouse	8 (52)	0.636	0.662	0.44	0.495	0.577	0.605	1.252	1.385	29.696	43.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.882	0.822	0.83	0.773	0.763	0.716
Overall, 4 experiments	best	0.915	0.866	0.864	0.815	0.784	0.748
Methyl HT-SELEX, 2 experiments	median	0.896	0.841	0.848	0.794	0.776	0.735
Methyl HT-SELEX, 2 experiments	best	0.915	0.866	0.864	0.815	0.784	0.748
Non-Methyl HT-SELEX, 2 experiments	median	0.876	0.815	0.823	0.766	0.753	0.71
Non-Methyl HT-SELEX, 2 experiments	best	0.887	0.828	0.827	0.774	0.758	0.711

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.0	1.429	0.301	0.025

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.71	0.314	0.569	0.423

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	SIX2.H13RSNP.2.SM.B.pcm
PWM	SIX2.H13RSNP.2.SM.B.pwm
PFM	SIX2.H13RSNP.2.SM.B.pfm
Threshold to P-value map	SIX2.H13RSNP.2.SM.B.thr
Motif in other formats
JASPAR format	SIX2.H13RSNP.2.SM.B_jaspar_format.txt
MEME format	SIX2.H13RSNP.2.SM.B_meme_format.meme
Transfac format	SIX2.H13RSNP.2.SM.B_transfac_format.txt
Homer format	SIX2.H13RSNP.2.SM.B_homer_format_0.001.txt SIX2.H13RSNP.2.SM.B_homer_format_0.0005.txt SIX2.H13RSNP.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	554.75	559.75	894.75	427.75
02	54.5	1026.5	291.5	1064.5
03	1.0	13.0	2423.0	0.0
04	2012.0	0.0	0.0	425.0
05	18.0	105.0	0.0	2314.0
06	2259.0	178.0	0.0	0.0
07	14.0	2107.0	83.0	233.0
08	256.0	1153.0	886.0	142.0
09	404.75	864.75	460.75	706.75

PFM

	A	C	G	T
01	0.228	0.23	0.367	0.176
02	0.022	0.421	0.12	0.437
03	0.0	0.005	0.994	0.0
04	0.826	0.0	0.0	0.174
05	0.007	0.043	0.0	0.95
06	0.927	0.073	0.0	0.0
07	0.006	0.865	0.034	0.096
08	0.105	0.473	0.364	0.058
09	0.166	0.355	0.189	0.29

PWM

	A	C	G	T
01	-0.093	-0.084	0.383	-0.352
02	-2.382	0.52	-0.734	0.557
03	-5.334	-3.711	1.378	-5.748
04	1.192	-5.748	-5.748	-0.359
05	-3.422	-1.743	-5.748	1.332
06	1.308	-1.223	-5.748	-5.748
07	-3.646	1.239	-1.973	-0.956
08	-0.863	0.636	0.373	-1.446
09	-0.407	0.349	-0.278	0.148

Standard thresholds

P-value	Threshold
0.001	5.211475
0.0005	6.04282
0.0001	7.473445