PHX2A.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PHX2A.H12INVIVO.1.SM.B
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	1
Quality	B

Motif length	12
Consensus	vnbYAATTAvbn
GC content	34.51%
Information content (bits; total / per base)	11.005 / 0.917
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7535

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)	0.833	0.866	0.686	0.718	0.76	0.795	2.174	2.338	52.184	87.495

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.964	0.942	0.945	0.916	0.914	0.878
Overall, 4 experiments	best	0.98	0.968	0.966	0.947	0.924	0.903
Methyl HT-SELEX, 1 experiments	median	0.96	0.934	0.944	0.912	0.914	0.878
Methyl HT-SELEX, 1 experiments	best	0.96	0.934	0.944	0.912	0.914	0.878
Non-Methyl HT-SELEX, 3 experiments	median	0.967	0.947	0.946	0.918	0.914	0.878
Non-Methyl HT-SELEX, 3 experiments	best	0.98	0.968	0.966	0.947	0.924	0.903

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.1.SM.B.pcm
PWM	PHX2A.H12INVIVO.1.SM.B.pwm
PFM	PHX2A.H12INVIVO.1.SM.B.pfm
Alignment	PHX2A.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	PHX2A.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	PHX2A.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	PHX2A.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	PHX2A.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	PHX2A.H12INVIVO.1.SM.B_homer_format_0.001.txt PHX2A.H12INVIVO.1.SM.B_homer_format_0.0005.txt PHX2A.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3028.25	1583.25	1655.25	1268.25
02	1587.5	2582.5	1375.5	1989.5
03	830.0	2860.0	2525.0	1320.0
04	349.0	2891.0	301.0	3994.0
05	6708.0	61.0	764.0	2.0
06	7535.0	0.0	0.0	0.0
07	0.0	0.0	0.0	7535.0
08	0.0	0.0	0.0	7535.0
09	7535.0	0.0	0.0	0.0
10	2463.0	1445.0	3431.0	196.0
11	469.75	3722.75	1767.75	1574.75
12	1286.25	1913.25	2326.25	2009.25

PFM

	A	C	G	T
01	0.402	0.21	0.22	0.168
02	0.211	0.343	0.183	0.264
03	0.11	0.38	0.335	0.175
04	0.046	0.384	0.04	0.53
05	0.89	0.008	0.101	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	1.0	0.0	0.0	0.0
10	0.327	0.192	0.455	0.026
11	0.062	0.494	0.235	0.209
12	0.171	0.254	0.309	0.267

PWM

	A	C	G	T
01	0.474	-0.174	-0.129	-0.395
02	-0.171	0.315	-0.314	0.055
03	-0.818	0.417	0.293	-0.355
04	-1.681	0.428	-1.828	0.751
05	1.269	-3.395	-0.901	-6.1
06	1.385	-6.739	-6.739	-6.739
07	-6.739	-6.739	-6.739	1.385
08	-6.739	-6.739	-6.739	1.385
09	1.385	-6.739	-6.739	-6.739
10	0.268	-0.265	0.599	-2.253
11	-1.385	0.681	-0.063	-0.179
12	-0.381	0.016	0.211	0.064

Standard thresholds

P-value	Threshold
0.001	4.314085
0.0005	5.76941
0.0001	7.84189