SIX2.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H12INVITRO.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	13
Consensus	GdMAhhdRAbMhn
GC content	43.41%
Information content (bits; total / per base)	7.849 / 0.604
Data sources	ChIP-Seq
Aligned words	1077

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)	0.896	0.918	0.817	0.855	0.891	0.915	3.288	3.645	211.681	261.538
Mouse	8 (52)	0.881	0.92	0.807	0.863	0.88	0.911	3.251	3.632	190.884	298.092

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.694	0.663	0.635	0.615	0.582	0.576
Overall, 4 experiments	best	0.886	0.848	0.788	0.756	0.68	0.673
Methyl HT-SELEX, 2 experiments	median	0.716	0.688	0.659	0.638	0.599	0.593
Methyl HT-SELEX, 2 experiments	best	0.886	0.848	0.788	0.756	0.68	0.673
Non-Methyl HT-SELEX, 2 experiments	median	0.687	0.658	0.63	0.611	0.578	0.574
Non-Methyl HT-SELEX, 2 experiments	best	0.841	0.796	0.741	0.709	0.647	0.639

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	23.75	3.398	0.421	0.321

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.771	0.489	0.792	0.595

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.H12INVITRO.0.P.B.pcm
PWM	SIX2.H12INVITRO.0.P.B.pwm
PFM	SIX2.H12INVITRO.0.P.B.pfm
Alignment	SIX2.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	SIX2.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	SIX2.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	SIX2.H12INVITRO.0.P.B_meme_format.meme
Transfac format	SIX2.H12INVITRO.0.P.B_transfac_format.txt
Homer format	SIX2.H12INVITRO.0.P.B_homer_format_0.001.txt SIX2.H12INVITRO.0.P.B_homer_format_0.0005.txt SIX2.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	46.0	46.0	935.0	50.0
02	465.0	105.0	145.0	362.0
03	788.0	149.0	71.0	69.0
04	1034.0	17.0	14.0	12.0
05	130.0	513.0	123.0	311.0
06	309.0	389.0	85.0	294.0
07	209.0	140.0	188.0	540.0
08	232.0	90.0	719.0	36.0
09	1042.0	10.0	12.0	13.0
10	155.0	176.0	355.0	391.0
11	523.0	398.0	77.0	79.0
12	125.0	568.0	122.0	262.0
13	176.0	409.0	222.0	270.0

PFM

	A	C	G	T
01	0.043	0.043	0.868	0.046
02	0.432	0.097	0.135	0.336
03	0.732	0.138	0.066	0.064
04	0.96	0.016	0.013	0.011
05	0.121	0.476	0.114	0.289
06	0.287	0.361	0.079	0.273
07	0.194	0.13	0.175	0.501
08	0.215	0.084	0.668	0.033
09	0.968	0.009	0.011	0.012
10	0.144	0.163	0.33	0.363
11	0.486	0.37	0.071	0.073
12	0.116	0.527	0.113	0.243
13	0.163	0.38	0.206	0.251

PWM

	A	C	G	T
01	-1.736	-1.736	1.24	-1.656
02	0.544	-0.932	-0.613	0.294
03	1.07	-0.587	-1.315	-1.343
04	1.341	-2.671	-2.846	-2.981
05	-0.721	0.642	-0.776	0.143
06	0.137	0.366	-1.139	0.087
07	-0.251	-0.648	-0.356	0.693
08	-0.148	-1.083	0.978	-1.971
09	1.348	-3.139	-2.981	-2.911
10	-0.547	-0.422	0.275	0.371
11	0.661	0.389	-1.236	-1.211
12	-0.76	0.743	-0.784	-0.027
13	-0.422	0.416	-0.192	0.003

Standard thresholds

P-value	Threshold
0.001	5.06016
0.0005	5.73601
0.0001	7.06456