CRX.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CRX.H12INVITRO.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	ndvGGATTAdbn
GC content	45.71%
Information content (bits; total / per base)	12.479 / 1.04
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	6715

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)	0.875	0.911	0.775	0.825	0.835	0.88	2.627	2.846	251.873	277.056

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.961	0.931	0.95	0.917	0.905	0.872
Overall, 2 experiments	best	0.967	0.94	0.951	0.922	0.912	0.876
Methyl HT-SELEX, 1 experiments	median	0.967	0.94	0.951	0.922	0.898	0.869
Methyl HT-SELEX, 1 experiments	best	0.967	0.94	0.951	0.922	0.898	0.869
Non-Methyl HT-SELEX, 1 experiments	median	0.955	0.921	0.948	0.911	0.912	0.876
Non-Methyl HT-SELEX, 1 experiments	best	0.955	0.921	0.948	0.911	0.912	0.876

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.845	0.78	0.877	0.677

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.H12INVITRO.0.PSM.A.pcm
PWM	CRX.H12INVITRO.0.PSM.A.pwm
PFM	CRX.H12INVITRO.0.PSM.A.pfm
Alignment	CRX.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	CRX.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	CRX.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	CRX.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	CRX.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	CRX.H12INVITRO.0.PSM.A_homer_format_0.001.txt CRX.H12INVITRO.0.PSM.A_homer_format_0.0005.txt CRX.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1573.0	1144.0	2258.0	1740.0
02	1837.25	792.25	2783.25	1302.25
03	1390.0	1395.0	2719.0	1211.0
04	174.0	0.0	6461.0	80.0
05	0.0	0.0	6715.0	0.0
06	6702.0	13.0	0.0	0.0
07	0.0	0.0	0.0	6715.0
08	0.0	0.0	0.0	6715.0
09	6715.0	0.0	0.0	0.0
10	1934.0	810.0	3030.0	941.0
11	526.75	1656.75	3110.75	1420.75
12	1134.5	1345.5	2599.5	1635.5

PFM

	A	C	G	T
01	0.234	0.17	0.336	0.259
02	0.274	0.118	0.414	0.194
03	0.207	0.208	0.405	0.18
04	0.026	0.0	0.962	0.012
05	0.0	0.0	1.0	0.0
06	0.998	0.002	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	1.0	0.0	0.0	0.0
10	0.288	0.121	0.451	0.14
11	0.078	0.247	0.463	0.212
12	0.169	0.2	0.387	0.244

PWM

	A	C	G	T
01	-0.065	-0.383	0.296	0.036
02	0.09	-0.749	0.505	-0.254
03	-0.188	-0.185	0.482	-0.326
04	-2.255	-6.637	1.347	-3.018
05	-6.637	-6.637	1.385	-6.637
06	1.383	-4.706	-6.637	-6.637
07	-6.637	-6.637	-6.637	1.385
08	-6.637	-6.637	-6.637	1.385
09	1.385	-6.637	-6.637	-6.637
10	0.141	-0.727	0.59	-0.578
11	-1.156	-0.013	0.616	-0.167
12	-0.391	-0.221	0.437	-0.026

Standard thresholds

P-value	Threshold
0.001	1.562265
0.0005	3.69418
0.0001	7.973665