OTX2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	OTX2.H12INVIVO.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	11
Consensus	vdvRGATTAdn
GC content	37.94%
Information content (bits; total / per base)	8.437 / 0.767
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	996

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)	0.934	0.962	0.866	0.916	0.883	0.913	2.858	3.148	228.854	415.796
Mouse	11 (69)	0.859	0.916	0.734	0.852	0.767	0.829	2.209	2.603	111.921	273.06

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.928	0.891	0.853	0.825	0.763	0.752
Overall, 4 experiments	best	0.977	0.96	0.967	0.946	0.934	0.91
Methyl HT-SELEX, 1 experiments	median	0.977	0.96	0.967	0.946	0.934	0.91
Methyl HT-SELEX, 1 experiments	best	0.977	0.96	0.967	0.946	0.934	0.91
Non-Methyl HT-SELEX, 3 experiments	median	0.903	0.863	0.772	0.754	0.643	0.657
Non-Methyl HT-SELEX, 3 experiments	best	0.953	0.92	0.934	0.897	0.883	0.847

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	20.808	36.647	0.394	0.373

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.H12INVIVO.0.PSM.A.pcm
PWM	OTX2.H12INVIVO.0.PSM.A.pwm
PFM	OTX2.H12INVIVO.0.PSM.A.pfm
Alignment	OTX2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	OTX2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	OTX2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	OTX2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	OTX2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	OTX2.H12INVIVO.0.PSM.A_homer_format_0.001.txt OTX2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt OTX2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	422.0	170.0	252.0	152.0
02	290.0	142.0	362.0	202.0
03	350.0	123.0	407.0	116.0
04	335.0	2.0	586.0	73.0
05	38.0	29.0	916.0	13.0
06	768.0	198.0	2.0	28.0
07	2.0	7.0	5.0	982.0
08	47.0	28.0	17.0	904.0
09	822.0	6.0	14.0	154.0
10	347.0	68.0	263.0	318.0
11	267.0	331.0	229.0	169.0

PFM

	A	C	G	T
01	0.424	0.171	0.253	0.153
02	0.291	0.143	0.363	0.203
03	0.351	0.123	0.409	0.116
04	0.336	0.002	0.588	0.073
05	0.038	0.029	0.92	0.013
06	0.771	0.199	0.002	0.028
07	0.002	0.007	0.005	0.986
08	0.047	0.028	0.017	0.908
09	0.825	0.006	0.014	0.155
10	0.348	0.068	0.264	0.319
11	0.268	0.332	0.23	0.17

PWM

	A	C	G	T
01	0.525	-0.378	0.012	-0.489
02	0.151	-0.556	0.372	-0.208
03	0.338	-0.698	0.489	-0.756
04	0.295	-4.209	0.852	-1.211
05	-1.842	-2.099	1.298	-2.835
06	1.122	-0.227	-4.209	-2.132
07	-4.209	-3.358	-3.618	1.367
08	-1.638	-2.132	-2.594	1.284
09	1.189	-3.48	-2.769	-0.476
10	0.33	-1.28	0.054	0.243
11	0.069	0.283	-0.083	-0.384

Standard thresholds

P-value	Threshold
0.001	5.1157
0.0005	5.940415
0.0001	7.30718