CRX.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CRX.H12RSNP.0.PSM.A
Gene (human)	CRX (GeneCards)
Gene synonyms (human)	CORD2
Gene (mouse)	Crx
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	ddGGATTAdnnn
GC content	42.81%
Information content (bits; total / per base)	10.665 / 0.889
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1002

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
Mouse	2 (14)	0.89	0.922	0.764	0.816	0.843	0.884	2.695	2.926	273.737	301.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.951	0.915	0.939	0.899	0.908	0.868
Overall, 2 experiments	best	0.956	0.924	0.941	0.905	0.914	0.87
Methyl HT-SELEX, 1 experiments	median	0.956	0.924	0.941	0.905	0.903	0.866
Methyl HT-SELEX, 1 experiments	best	0.956	0.924	0.941	0.905	0.903	0.866
Non-Methyl HT-SELEX, 1 experiments	median	0.945	0.906	0.936	0.894	0.914	0.87
Non-Methyl HT-SELEX, 1 experiments	best	0.945	0.906	0.936	0.894	0.914	0.87

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.859	0.776	0.89	0.696

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	OTX {3.1.3.17} (TFClass)
TFClass ID	TFClass: 3.1.3.17.3
HGNC	HGNC:2383
MGI	MGI:1194883
EntrezGene (human)	GeneID:1406 (SSTAR profile)
EntrezGene (mouse)	GeneID:12951 (SSTAR profile)
UniProt ID (human)	CRX_HUMAN
UniProt ID (mouse)	CRX_MOUSE
UniProt AC (human)	O43186 (TFClass)
UniProt AC (mouse)	O54751 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	CRX.H12RSNP.0.PSM.A.pcm
PWM	CRX.H12RSNP.0.PSM.A.pwm
PFM	CRX.H12RSNP.0.PSM.A.pfm
Alignment	CRX.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	CRX.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	CRX.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	CRX.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	CRX.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	CRX.H12RSNP.0.PSM.A_homer_format_0.001.txt CRX.H12RSNP.0.PSM.A_homer_format_0.0005.txt CRX.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	256.0	113.0	439.0	194.0
02	404.0	83.0	430.0	85.0
03	276.0	2.0	720.0	4.0
04	9.0	6.0	984.0	3.0
05	809.0	191.0	0.0	2.0
06	0.0	0.0	0.0	1002.0
07	7.0	13.0	3.0	979.0
08	970.0	2.0	1.0	29.0
09	361.0	65.0	415.0	161.0
10	274.0	272.0	285.0	171.0
11	236.0	224.0	352.0	190.0
12	257.0	235.0	312.0	198.0

PFM

	A	C	G	T
01	0.255	0.113	0.438	0.194
02	0.403	0.083	0.429	0.085
03	0.275	0.002	0.719	0.004
04	0.009	0.006	0.982	0.003
05	0.807	0.191	0.0	0.002
06	0.0	0.0	0.0	1.0
07	0.007	0.013	0.003	0.977
08	0.968	0.002	0.001	0.029
09	0.36	0.065	0.414	0.161
10	0.273	0.271	0.284	0.171
11	0.236	0.224	0.351	0.19
12	0.256	0.235	0.311	0.198

PWM

	A	C	G	T
01	0.022	-0.788	0.558	-0.254
02	0.475	-1.091	0.537	-1.068
03	0.096	-4.215	1.051	-3.785
04	-3.158	-3.486	1.363	-3.977
05	1.168	-0.269	-4.984	-4.215
06	-4.984	-4.984	-4.984	1.381
07	-3.364	-2.841	-3.977	1.358
08	1.349	-4.215	-4.527	-2.105
09	0.363	-1.33	0.502	-0.438
10	0.089	0.082	0.128	-0.379
11	-0.059	-0.111	0.338	-0.274
12	0.025	-0.063	0.218	-0.233

Standard thresholds

P-value	Threshold
0.001	4.289115
0.0005	5.7771
0.0001	7.72968