SIX2.H12RSNP.1.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H12RSNP.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	bKWhMYvYGATAYSn
GC content	48.64%
Information content (bits; total / per base)	13.097 / 0.873
Data sources	Methyl-HT-SELEX
Aligned words	334

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)	0.724	0.752	0.598	0.654	0.726	0.762	2.195	2.508	105.221	132.42
Mouse	8 (52)	0.727	0.776	0.61	0.677	0.71	0.759	2.124	2.433	102.09	184.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.885	0.836	0.828	0.778	0.754	0.716
Overall, 4 experiments	best	0.918	0.889	0.848	0.812	0.765	0.737
Methyl HT-SELEX, 2 experiments	median	0.896	0.852	0.835	0.789	0.757	0.723
Methyl HT-SELEX, 2 experiments	best	0.918	0.889	0.848	0.812	0.765	0.737
Non-Methyl HT-SELEX, 2 experiments	median	0.871	0.819	0.812	0.761	0.74	0.702
Non-Methyl HT-SELEX, 2 experiments	best	0.896	0.856	0.833	0.789	0.758	0.723

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.5	1.187	0.277	0.093

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.672	0.412	0.662	0.492

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.H12RSNP.1.M.C.pcm
PWM	SIX2.H12RSNP.1.M.C.pwm
PFM	SIX2.H12RSNP.1.M.C.pfm
Alignment	SIX2.H12RSNP.1.M.C.words.tsv
Threshold to P-value map	SIX2.H12RSNP.1.M.C.thr
Motif in other formats
JASPAR format	SIX2.H12RSNP.1.M.C_jaspar_format.txt
MEME format	SIX2.H12RSNP.1.M.C_meme_format.meme
Transfac format	SIX2.H12RSNP.1.M.C_transfac_format.txt
Homer format	SIX2.H12RSNP.1.M.C_homer_format_0.001.txt SIX2.H12RSNP.1.M.C_homer_format_0.0005.txt SIX2.H12RSNP.1.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	42.0	135.0	70.0	87.0
02	30.5	22.5	247.5	33.5
03	84.0	41.0	15.0	194.0
04	178.0	40.0	27.0	89.0
05	259.0	31.0	17.0	27.0
06	18.0	242.0	36.0	38.0
07	59.0	88.0	153.0	34.0
08	2.0	168.0	4.0	160.0
09	3.0	0.0	331.0	0.0
10	329.0	0.0	2.0	3.0
11	2.0	11.0	0.0	321.0
12	321.0	9.0	4.0	0.0
13	3.0	251.0	26.0	54.0
14	10.0	157.0	137.0	30.0
15	61.5	88.5	83.5	100.5

PFM

	A	C	G	T
01	0.126	0.404	0.21	0.26
02	0.091	0.067	0.741	0.1
03	0.251	0.123	0.045	0.581
04	0.533	0.12	0.081	0.266
05	0.775	0.093	0.051	0.081
06	0.054	0.725	0.108	0.114
07	0.177	0.263	0.458	0.102
08	0.006	0.503	0.012	0.479
09	0.009	0.0	0.991	0.0
10	0.985	0.0	0.006	0.009
11	0.006	0.033	0.0	0.961
12	0.961	0.027	0.012	0.0
13	0.009	0.751	0.078	0.162
14	0.03	0.47	0.41	0.09
15	0.184	0.265	0.25	0.301

PWM

	A	C	G	T
01	-0.67	0.474	-0.173	0.04
02	-0.978	-1.266	1.075	-0.888
03	0.006	-0.694	-1.642	0.833
04	0.748	-0.718	-1.094	0.063
05	1.12	-0.962	-1.527	-1.094
06	-1.474	1.053	-0.819	-0.767
07	-0.34	0.052	0.598	-0.874
08	-3.203	0.69	-2.746	0.642
09	-2.949	-4.069	1.364	-4.069
10	1.358	-4.069	-3.203	-2.949
11	-3.203	-1.92	-4.069	1.334
12	1.334	-2.095	-2.746	-4.069
13	-2.949	1.089	-1.13	-0.427
14	-2.004	0.623	0.488	-0.994
15	-0.3	0.057	0.0	0.182

Standard thresholds

P-value	Threshold
0.001	3.91761
0.0005	4.96291
0.0001	7.10316