SIX2.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H12INVIVO.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	14
Consensus	KGWAAYhYRAbMYb
GC content	40.82%
Information content (bits; total / per base)	11.933 / 0.852
Data sources	ChIP-Seq
Aligned words	1000

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)	0.913	0.935	0.829	0.872	0.914	0.935	3.494	3.904	244.071	287.796
Mouse	8 (52)	0.901	0.936	0.828	0.882	0.898	0.934	3.437	3.902	220.284	340.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.679	0.654	0.625	0.607	0.578	0.572
Overall, 4 experiments	best	0.867	0.829	0.764	0.734	0.664	0.657
Methyl HT-SELEX, 2 experiments	median	0.695	0.673	0.641	0.623	0.589	0.583
Methyl HT-SELEX, 2 experiments	best	0.867	0.829	0.764	0.734	0.664	0.657
Non-Methyl HT-SELEX, 2 experiments	median	0.676	0.651	0.623	0.606	0.576	0.571
Non-Methyl HT-SELEX, 2 experiments	best	0.834	0.791	0.732	0.702	0.643	0.635

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	27.273	3.862	0.433	0.313

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.744	0.504	0.798	0.612

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.H12INVIVO.0.P.B.pcm
PWM	SIX2.H12INVIVO.0.P.B.pwm
PFM	SIX2.H12INVIVO.0.P.B.pfm
Alignment	SIX2.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	SIX2.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	SIX2.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	SIX2.H12INVIVO.0.P.B_meme_format.meme
Transfac format	SIX2.H12INVIVO.0.P.B_transfac_format.txt
Homer format	SIX2.H12INVIVO.0.P.B_homer_format_0.001.txt SIX2.H12INVIVO.0.P.B_homer_format_0.0005.txt SIX2.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	196.0	7.0	261.0	536.0
02	7.0	1.0	981.0	11.0
03	479.0	43.0	70.0	408.0
04	888.0	61.0	4.0	47.0
05	997.0	1.0	2.0	0.0
06	38.0	546.0	57.0	359.0
07	162.0	415.0	63.0	360.0
08	99.0	118.0	104.0	679.0
09	166.0	12.0	764.0	58.0
10	996.0	1.0	3.0	0.0
11	63.0	180.0	309.0	448.0
12	501.0	411.0	23.0	65.0
13	101.0	587.0	75.0	237.0
14	148.0	423.0	193.0	236.0

PFM

	A	C	G	T
01	0.196	0.007	0.261	0.536
02	0.007	0.001	0.981	0.011
03	0.479	0.043	0.07	0.408
04	0.888	0.061	0.004	0.047
05	0.997	0.001	0.002	0.0
06	0.038	0.546	0.057	0.359
07	0.162	0.415	0.063	0.36
08	0.099	0.118	0.104	0.679
09	0.166	0.012	0.764	0.058
10	0.996	0.001	0.003	0.0
11	0.063	0.18	0.309	0.448
12	0.501	0.411	0.023	0.065
13	0.101	0.587	0.075	0.237
14	0.148	0.423	0.193	0.236

PWM

	A	C	G	T
01	-0.241	-3.362	0.043	0.759
02	-3.362	-4.525	1.362	-2.985
03	0.647	-1.728	-1.255	0.487
04	1.263	-1.39	-3.783	-1.642
05	1.378	-4.525	-4.213	-4.982
06	-1.846	0.777	-1.455	0.36
07	-0.43	0.504	-1.358	0.363
08	-0.916	-0.743	-0.867	0.995
09	-0.406	-2.909	1.112	-1.439
10	1.377	-4.525	-3.975	-4.982
11	-1.358	-0.326	0.211	0.58
12	0.692	0.494	-2.32	-1.328
13	-0.896	0.85	-1.188	-0.053
14	-0.52	0.523	-0.257	-0.057

Standard thresholds

P-value	Threshold
0.001	4.17661
0.0005	5.23411
0.0001	7.30851