SIX2.H14INVITRO.1.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H14INVITRO.1.M.C
Gene (human)	SIX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Six2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	15
Consensus	bKhhWYvYGATACSn
GC content	48.87%
Information content (bits; total / per base)	12.616 / 0.841
Data sources	Methyl-HT-SELEX
Aligned words	607
Previous names	SIX2.H12INVITRO.1.M.C

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)	0.711	0.742	0.574	0.635	0.705	0.743	2.039	2.346	93.256	115.77
Mouse	8 (52)	0.714	0.76	0.585	0.651	0.687	0.735	1.98	2.254	94.723	164.469

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.892	0.843	0.837	0.787	0.761	0.724
Overall, 4 experiments	best	0.918	0.887	0.853	0.814	0.769	0.74
Methyl HT-SELEX, 2 experiments	median	0.902	0.859	0.845	0.799	0.765	0.731
Methyl HT-SELEX, 2 experiments	best	0.918	0.887	0.853	0.814	0.769	0.74
Non-Methyl HT-SELEX, 2 experiments	median	0.878	0.827	0.821	0.77	0.746	0.709
Non-Methyl HT-SELEX, 2 experiments	best	0.896	0.856	0.837	0.791	0.761	0.726

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.03	0.914	0.266	0.08

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.681	0.406	0.626	0.476

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.H14INVITRO.1.M.C.pcm
PWM	SIX2.H14INVITRO.1.M.C.pwm
PFM	SIX2.H14INVITRO.1.M.C.pfm
Threshold to P-value map	SIX2.H14INVITRO.1.M.C.thr
Motif in other formats
JASPAR format	SIX2.H14INVITRO.1.M.C_jaspar_format.txt
MEME format	SIX2.H14INVITRO.1.M.C_meme_format.meme
Transfac format	SIX2.H14INVITRO.1.M.C_transfac_format.txt
Homer format	SIX2.H14INVITRO.1.M.C_homer_format_0.001.txt SIX2.H14INVITRO.1.M.C_homer_format_0.0005.txt SIX2.H14INVITRO.1.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	88.25	242.25	102.25	174.25
02	67.5	63.5	400.5	75.5
03	135.0	93.0	46.0	333.0
04	309.0	103.0	53.0	142.0
05	442.0	54.0	48.0	63.0
06	47.0	410.0	64.0	86.0
07	122.0	145.0	269.0	71.0
08	5.0	311.0	8.0	283.0
09	3.0	0.0	604.0	0.0
10	603.0	0.0	0.0	4.0
11	3.0	25.0	0.0	579.0
12	594.0	12.0	1.0	0.0
13	5.0	477.0	46.0	79.0
14	22.5	280.5	265.5	38.5
15	104.75	172.75	153.75	175.75

PFM

	A	C	G	T
01	0.145	0.399	0.168	0.287
02	0.111	0.105	0.66	0.124
03	0.222	0.153	0.076	0.549
04	0.509	0.17	0.087	0.234
05	0.728	0.089	0.079	0.104
06	0.077	0.675	0.105	0.142
07	0.201	0.239	0.443	0.117
08	0.008	0.512	0.013	0.466
09	0.005	0.0	0.995	0.0
10	0.993	0.0	0.0	0.007
11	0.005	0.041	0.0	0.954
12	0.979	0.02	0.002	0.0
13	0.008	0.786	0.076	0.13
14	0.037	0.462	0.437	0.063
15	0.173	0.285	0.253	0.29

PWM

	A	C	G	T
01	-0.535	0.464	-0.39	0.137
02	-0.797	-0.857	0.964	-0.688
03	-0.116	-0.483	-1.17	0.78
04	0.706	-0.383	-1.033	-0.066
05	1.062	-1.015	-1.129	-0.864
06	-1.149	0.987	-0.849	-0.56
07	-0.216	-0.045	0.568	-0.748
08	-3.145	0.712	-2.771	0.618
09	-3.506	-4.561	1.373	-4.561
10	1.372	-4.561	-4.561	-3.31
11	-3.506	-1.752	-4.561	1.331
12	1.357	-2.423	-4.076	-4.561
13	-3.145	1.138	-1.17	-0.643
14	-1.85	0.61	0.555	-1.341
15	-0.366	0.128	0.013	0.145

Standard thresholds

P-value	Threshold
0.001	3.96096
0.0005	5.05756
0.0001	7.22471