OTX2.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	OTX2.H12INVITRO.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	41.52%
Information content (bits; total / per base)	10.802 / 1.08
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)	0.912	0.943	0.828	0.88	0.869	0.898	2.752	3.055	193.699	392.658
Mouse	11 (69)	0.845	0.9	0.726	0.811	0.772	0.837	2.231	2.738	111.658	262.337

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.933	0.899	0.858	0.831	0.766	0.756
Overall, 4 experiments	best	0.98	0.966	0.97	0.952	0.94	0.918
Methyl HT-SELEX, 1 experiments	median	0.98	0.966	0.97	0.952	0.94	0.918
Methyl HT-SELEX, 1 experiments	best	0.98	0.966	0.97	0.952	0.94	0.918
Non-Methyl HT-SELEX, 3 experiments	median	0.906	0.867	0.776	0.757	0.647	0.66
Non-Methyl HT-SELEX, 3 experiments	best	0.959	0.93	0.939	0.906	0.886	0.853

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	24.811	39.987	0.404	0.382

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.H12INVITRO.0.PSM.A.pcm
PWM	OTX2.H12INVITRO.0.PSM.A.pwm
PFM	OTX2.H12INVITRO.0.PSM.A.pfm
Alignment	OTX2.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	OTX2.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	OTX2.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	OTX2.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	OTX2.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	OTX2.H12INVITRO.0.PSM.A_homer_format_0.001.txt OTX2.H12INVITRO.0.PSM.A_homer_format_0.0005.txt OTX2.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	365.0	78.0	397.0	160.0
02	325.0	81.0	534.0	60.0
03	188.0	6.0	795.0	11.0
04	39.0	17.0	940.0	4.0
05	872.0	123.0	2.0	3.0
06	3.0	0.0	0.0	997.0
07	13.0	6.0	2.0	979.0
08	943.0	0.0	7.0	50.0
09	413.0	60.0	411.0	116.0
10	213.0	355.0	338.0	94.0

PFM

	A	C	G	T
01	0.365	0.078	0.397	0.16
02	0.325	0.081	0.534	0.06
03	0.188	0.006	0.795	0.011
04	0.039	0.017	0.94	0.004
05	0.872	0.123	0.002	0.003
06	0.003	0.0	0.0	0.997
07	0.013	0.006	0.002	0.979
08	0.943	0.0	0.007	0.05
09	0.413	0.06	0.411	0.116
10	0.213	0.355	0.338	0.094

PWM

	A	C	G	T
01	0.376	-1.15	0.46	-0.442
02	0.261	-1.113	0.755	-1.406
03	-0.283	-3.484	1.152	-2.985
04	-1.821	-2.598	1.319	-3.783
05	1.244	-0.702	-4.213	-3.975
06	-3.975	-4.982	-4.982	1.378
07	-2.839	-3.484	-4.213	1.36
08	1.323	-4.982	-3.362	-1.582
09	0.499	-1.406	0.494	-0.76
10	-0.159	0.349	0.3	-0.967

Standard thresholds

P-value	Threshold
0.001	4.4825
0.0005	5.522545
0.0001	7.679135