OTX1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	OTX1.H12INVIVO.0.SM.D
Gene (human)	OTX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Otx1
Gene synonyms (mouse)	Otx-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	dnvSGATTAdnn
GC content	41.44%
Information content (bits; total / per base)	11.282 / 0.94
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8976

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.948	0.91	0.922	0.884	0.858	0.824
Overall, 10 experiments	best	0.99	0.983	0.984	0.974	0.967	0.953
Methyl HT-SELEX, 3 experiments	median	0.945	0.904	0.928	0.886	0.883	0.841
Methyl HT-SELEX, 3 experiments	best	0.989	0.98	0.984	0.973	0.952	0.939
Non-Methyl HT-SELEX, 7 experiments	median	0.951	0.916	0.917	0.883	0.833	0.807
Non-Methyl HT-SELEX, 7 experiments	best	0.99	0.983	0.984	0.974	0.967	0.953

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.996	0.929	0.966	0.558
batch 2	0.852	0.72	0.889	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: 3.1.3.17.1
HGNC	HGNC:8521
MGI	MGI:97450
EntrezGene (human)	GeneID:5013 (SSTAR profile)
EntrezGene (mouse)	GeneID:18423 (SSTAR profile)
UniProt ID (human)	OTX1_HUMAN
UniProt ID (mouse)	OTX1_MOUSE
UniProt AC (human)	P32242 (TFClass)
UniProt AC (mouse)	P80205 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	7
Methyl-HT-SELEX	3

PCM	OTX1.H12INVIVO.0.SM.D.pcm
PWM	OTX1.H12INVIVO.0.SM.D.pwm
PFM	OTX1.H12INVIVO.0.SM.D.pfm
Alignment	OTX1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	OTX1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	OTX1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	OTX1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	OTX1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	OTX1.H12INVIVO.0.SM.D_homer_format_0.001.txt OTX1.H12INVIVO.0.SM.D_homer_format_0.0005.txt OTX1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3910.5	1623.5	1699.5	1742.5
02	1844.0	1713.0	2947.0	2472.0
03	1476.0	4578.0	2068.0	854.0
04	891.0	943.0	6941.0	201.0
05	0.0	2.0	8974.0	0.0
06	8704.0	272.0	0.0	0.0
07	0.0	0.0	0.0	8976.0
08	2.0	0.0	0.0	8974.0
09	8915.0	0.0	7.0	54.0
10	4142.0	1108.0	2042.0	1684.0
11	1631.25	2410.25	2716.25	2218.25
12	2153.5	1884.5	2702.5	2235.5

PFM

	A	C	G	T
01	0.436	0.181	0.189	0.194
02	0.205	0.191	0.328	0.275
03	0.164	0.51	0.23	0.095
04	0.099	0.105	0.773	0.022
05	0.0	0.0	1.0	0.0
06	0.97	0.03	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.993	0.0	0.001	0.006
10	0.461	0.123	0.227	0.188
11	0.182	0.269	0.303	0.247
12	0.24	0.21	0.301	0.249

PWM

	A	C	G	T
01	0.555	-0.323	-0.278	-0.253
02	-0.196	-0.27	0.272	0.097
03	-0.418	0.712	-0.082	-0.964
04	-0.922	-0.866	1.129	-2.402
05	-6.895	-6.264	1.385	-6.895
06	1.355	-2.103	-6.895	-6.895
07	-6.895	-6.895	-6.895	1.386
08	-6.264	-6.895	-6.895	1.385
09	1.379	-6.895	-5.49	-3.687
10	0.612	-0.705	-0.094	-0.287
11	-0.319	0.071	0.191	-0.012
12	-0.041	-0.174	0.186	-0.004

Standard thresholds

P-value	Threshold
0.001	4.00628
0.0005	5.60162
0.0001	7.821405