PHX2A.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PHX2A.H12INVIVO.0.PS.A
Gene (human)	PHOX2A (GeneCards)
Gene synonyms (human)	ARIX, PMX2A
Gene (mouse)	Phox2a
Gene synonyms (mouse)	Arix, Phox2, Pmx2, Pmx2a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	14
Consensus	bWAATYYWATTAvv
GC content	26.71%
Information content (bits; total / per base)	12.577 / 0.898
Data sources	ChIP-Seq + HT-SELEX
Aligned words	138

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	1 (4)	0.896	0.947	0.839	0.908	0.888	0.944	3.77	4.382	110.288	180.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.975	0.958	0.954	0.931	0.906	0.877
Overall, 4 experiments	best	0.994	0.99	0.986	0.979	0.91	0.904
Methyl HT-SELEX, 1 experiments	median	0.967	0.943	0.949	0.92	0.91	0.878
Methyl HT-SELEX, 1 experiments	best	0.967	0.943	0.949	0.92	0.91	0.878
Non-Methyl HT-SELEX, 3 experiments	median	0.982	0.971	0.959	0.942	0.904	0.877
Non-Methyl HT-SELEX, 3 experiments	best	0.994	0.99	0.986	0.979	0.908	0.904

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	PHOX {3.1.3.18} (TFClass)
TFClass ID	TFClass: 3.1.3.18.1
HGNC	HGNC:691
MGI	MGI:106633
EntrezGene (human)	GeneID:401 (SSTAR profile)
EntrezGene (mouse)	GeneID:11859 (SSTAR profile)
UniProt ID (human)	PHX2A_HUMAN
UniProt ID (mouse)	PHX2A_MOUSE
UniProt AC (human)	O14813 (TFClass)
UniProt AC (mouse)	Q62066 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	PHX2A.H12INVIVO.0.PS.A.pcm
PWM	PHX2A.H12INVIVO.0.PS.A.pwm
PFM	PHX2A.H12INVIVO.0.PS.A.pfm
Alignment	PHX2A.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	PHX2A.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	PHX2A.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	PHX2A.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	PHX2A.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	PHX2A.H12INVIVO.0.PS.A_homer_format_0.001.txt PHX2A.H12INVIVO.0.PS.A_homer_format_0.0005.txt PHX2A.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	15.0	51.0	26.0	46.0
02	46.0	14.0	2.0	76.0
03	124.0	3.0	8.0	3.0
04	129.0	4.0	5.0	0.0
05	6.0	7.0	10.0	115.0
06	1.0	80.0	28.0	29.0
07	7.0	63.0	7.0	61.0
08	104.0	8.0	9.0	17.0
09	113.0	5.0	10.0	10.0
10	0.0	0.0	1.0	137.0
11	3.0	6.0	2.0	127.0
12	110.0	0.0	2.0	26.0
13	41.0	25.0	52.0	20.0
14	30.0	61.0	27.0	20.0

PFM

	A	C	G	T
01	0.109	0.37	0.188	0.333
02	0.333	0.101	0.014	0.551
03	0.899	0.022	0.058	0.022
04	0.935	0.029	0.036	0.0
05	0.043	0.051	0.072	0.833
06	0.007	0.58	0.203	0.21
07	0.051	0.457	0.051	0.442
08	0.754	0.058	0.065	0.123
09	0.819	0.036	0.072	0.072
10	0.0	0.0	0.007	0.993
11	0.022	0.043	0.014	0.92
12	0.797	0.0	0.014	0.188
13	0.297	0.181	0.377	0.145
14	0.217	0.442	0.196	0.145

PWM

	A	C	G	T
01	-0.789	0.38	-0.272	0.279
02	0.279	-0.853	-2.403	0.771
03	1.254	-2.133	-1.353	-2.133
04	1.293	-1.921	-1.746	-3.368
05	-1.598	-1.468	-1.157	1.18
06	-2.773	0.821	-0.201	-0.167
07	-1.468	0.586	-1.468	0.555
08	1.08	-1.353	-1.251	-0.673
09	1.162	-1.746	-1.157	-1.157
10	-3.368	-3.368	-2.773	1.353
11	-2.133	-1.598	-2.403	1.278
12	1.136	-3.368	-2.403	-0.272
13	0.167	-0.309	0.399	-0.521
14	-0.135	0.555	-0.236	-0.521

Standard thresholds

P-value	Threshold
0.001	4.29256
0.0005	5.21796
0.0001	7.13031