CRX.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CRX.H12INVIVO.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	13
Consensus	hvRdvRGATTAdv
GC content	41.39%
Information content (bits; total / per base)	10.621 / 0.817
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1001

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)	0.926	0.943	0.855	0.885	0.861	0.889	2.833	3.092	276.278	314.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.943	0.902	0.928	0.884	0.894	0.849
Overall, 2 experiments	best	0.946	0.908	0.928	0.887	0.899	0.852
Methyl HT-SELEX, 1 experiments	median	0.946	0.908	0.928	0.887	0.889	0.847
Methyl HT-SELEX, 1 experiments	best	0.946	0.908	0.928	0.887	0.889	0.847
Non-Methyl HT-SELEX, 1 experiments	median	0.939	0.895	0.927	0.88	0.899	0.852
Non-Methyl HT-SELEX, 1 experiments	best	0.939	0.895	0.927	0.88	0.899	0.852

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.862	0.743	0.859	0.671

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.H12INVIVO.0.PSM.A.pcm
PWM	CRX.H12INVIVO.0.PSM.A.pwm
PFM	CRX.H12INVIVO.0.PSM.A.pfm
Alignment	CRX.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	CRX.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	CRX.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	CRX.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	CRX.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	CRX.H12INVIVO.0.PSM.A_homer_format_0.001.txt CRX.H12INVIVO.0.PSM.A_homer_format_0.0005.txt CRX.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	256.0	161.0	140.0	444.0
02	525.0	152.0	246.0	78.0
03	605.0	57.0	232.0	107.0
04	160.0	90.0	576.0	175.0
05	425.0	193.0	310.0	73.0
06	264.0	13.0	698.0	26.0
07	10.0	9.0	972.0	10.0
08	732.0	263.0	3.0	3.0
09	0.0	0.0	0.0	1001.0
10	20.0	34.0	7.0	940.0
11	874.0	2.0	28.0	97.0
12	315.0	90.0	464.0	132.0
13	239.0	301.0	345.0	116.0

PFM

	A	C	G	T
01	0.256	0.161	0.14	0.444
02	0.524	0.152	0.246	0.078
03	0.604	0.057	0.232	0.107
04	0.16	0.09	0.575	0.175
05	0.425	0.193	0.31	0.073
06	0.264	0.013	0.697	0.026
07	0.01	0.009	0.971	0.01
08	0.731	0.263	0.003	0.003
09	0.0	0.0	0.0	1.0
10	0.02	0.034	0.007	0.939
11	0.873	0.002	0.028	0.097
12	0.315	0.09	0.464	0.132
13	0.239	0.301	0.345	0.116

PWM

	A	C	G	T
01	0.023	-0.437	-0.575	0.57
02	0.737	-0.494	-0.017	-1.151
03	0.879	-1.456	-0.075	-0.84
04	-0.443	-1.011	0.83	-0.355
05	0.527	-0.258	0.213	-1.215
06	0.053	-2.84	1.021	-2.207
07	-3.067	-3.157	1.352	-3.067
08	1.069	0.049	-3.976	-3.976
09	-4.983	-4.983	-4.983	1.381
10	-2.451	-1.953	-3.363	1.318
11	1.246	-4.214	-2.137	-0.937
12	0.229	-1.011	0.614	-0.634
13	-0.046	0.183	0.319	-0.761

Standard thresholds

P-value	Threshold
0.001	4.61961
0.0005	5.58501
0.0001	7.428915