OTX2.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	OTX2.H12RSNP.0.PSM.A
Gene (human)	OTX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Otx2
Gene synonyms (mouse)	Otx-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	10
Consensus	dRGGATTAdv
GC content	41.39%
Information content (bits; total / per base)	10.71 / 1.071
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000

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	19 (125)	0.913	0.943	0.828	0.879	0.869	0.899	2.779	3.102	189.509	384.77
Mouse	11 (69)	0.844	0.901	0.725	0.812	0.773	0.836	2.246	2.751	111.602	262.337

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.932	0.898	0.857	0.831	0.764	0.755
Overall, 4 experiments	best	0.98	0.965	0.97	0.952	0.939	0.917
Methyl HT-SELEX, 1 experiments	median	0.98	0.965	0.97	0.952	0.939	0.917
Methyl HT-SELEX, 1 experiments	best	0.98	0.965	0.97	0.952	0.939	0.917
Non-Methyl HT-SELEX, 3 experiments	median	0.907	0.867	0.775	0.756	0.645	0.659
Non-Methyl HT-SELEX, 3 experiments	best	0.958	0.929	0.94	0.906	0.884	0.851

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	24.349	39.495	0.402	0.385

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: 3.1.3.17.2
HGNC	HGNC:8522
MGI	MGI:97451
EntrezGene (human)	GeneID:5015 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	OTX2_HUMAN
UniProt ID (mouse)	OTX2_MOUSE
UniProt AC (human)	P32243 (TFClass)
UniProt AC (mouse)	P80206 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	19 human, 11 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	OTX2.H12RSNP.0.PSM.A.pcm
PWM	OTX2.H12RSNP.0.PSM.A.pwm
PFM	OTX2.H12RSNP.0.PSM.A.pfm
Alignment	OTX2.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	OTX2.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	OTX2.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	OTX2.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	OTX2.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	OTX2.H12RSNP.0.PSM.A_homer_format_0.001.txt OTX2.H12RSNP.0.PSM.A_homer_format_0.0005.txt OTX2.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	373.0	71.0	402.0	154.0
02	326.0	85.0	537.0	52.0
03	200.0	8.0	780.0	12.0
04	36.0	12.0	948.0	4.0
05	867.0	125.0	4.0	4.0
06	3.0	0.0	1.0	996.0
07	15.0	11.0	6.0	968.0
08	949.0	4.0	8.0	39.0
09	419.0	55.0	402.0	124.0
10	220.0	348.0	332.0	100.0

PFM

	A	C	G	T
01	0.373	0.071	0.402	0.154
02	0.326	0.085	0.537	0.052
03	0.2	0.008	0.78	0.012
04	0.036	0.012	0.948	0.004
05	0.867	0.125	0.004	0.004
06	0.003	0.0	0.001	0.996
07	0.015	0.011	0.006	0.968
08	0.949	0.004	0.008	0.039
09	0.419	0.055	0.402	0.124
10	0.22	0.348	0.332	0.1

PWM

	A	C	G	T
01	0.398	-1.242	0.472	-0.48
02	0.264	-1.066	0.761	-1.544
03	-0.221	-3.253	1.133	-2.909
04	-1.898	-2.909	1.328	-3.783
05	1.239	-0.686	-3.783	-3.783
06	-3.975	-4.982	-4.525	1.377
07	-2.711	-2.985	-3.484	1.349
08	1.329	-3.783	-3.253	-1.821
09	0.514	-1.49	0.472	-0.694
10	-0.127	0.329	0.282	-0.906

Standard thresholds

P-value	Threshold
0.001	4.47154
0.0005	5.47575
0.0001	7.61167