PHX2B.H12RSNP.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PHX2B.H12RSNP.1.SM.D
Gene (human)	PHOX2B (GeneCards)
Gene synonyms (human)	PMX2B
Gene (mouse)	Phox2b
Gene synonyms (mouse)	Pmx2b
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	11
Consensus	nvbTAATTvvn
GC content	31.28%
Information content (bits; total / per base)	10.654 / 0.969
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7097

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	3 (21)	0.864	0.948	0.765	0.902	0.688	0.805	1.732	2.206	103.824	136.268

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.955	0.926	0.925	0.893	0.842	0.801
Overall, 8 experiments	best	0.978	0.959	0.974	0.954	0.953	0.931
Methyl HT-SELEX, 2 experiments	median	0.94	0.9	0.908	0.867	0.8	0.782
Methyl HT-SELEX, 2 experiments	best	0.967	0.94	0.931	0.903	0.841	0.788
Non-Methyl HT-SELEX, 6 experiments	median	0.955	0.926	0.933	0.899	0.878	0.846
Non-Methyl HT-SELEX, 6 experiments	best	0.978	0.959	0.974	0.954	0.953	0.931

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: 3.1.3.18.2
HGNC	HGNC:9143
MGI	MGI:1100882
EntrezGene (human)	GeneID:8929 (SSTAR profile)
EntrezGene (mouse)	GeneID:18935 (SSTAR profile)
UniProt ID (human)	PHX2B_HUMAN
UniProt ID (mouse)	PHX2B_MOUSE
UniProt AC (human)	Q99453 (TFClass)
UniProt AC (mouse)	O35690 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	PHX2B.H12RSNP.1.SM.D.pcm
PWM	PHX2B.H12RSNP.1.SM.D.pwm
PFM	PHX2B.H12RSNP.1.SM.D.pfm
Alignment	PHX2B.H12RSNP.1.SM.D.words.tsv
Threshold to P-value map	PHX2B.H12RSNP.1.SM.D.thr
Motif in other formats
JASPAR format	PHX2B.H12RSNP.1.SM.D_jaspar_format.txt
MEME format	PHX2B.H12RSNP.1.SM.D_meme_format.meme
Transfac format	PHX2B.H12RSNP.1.SM.D_transfac_format.txt
Homer format	PHX2B.H12RSNP.1.SM.D_homer_format_0.001.txt PHX2B.H12RSNP.1.SM.D_homer_format_0.0005.txt PHX2B.H12RSNP.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1967.0	2117.0	1780.0	1233.0
02	1629.0	2244.0	2638.0	586.0
03	134.0	2753.0	1293.0	2917.0
04	0.0	0.0	0.0	7097.0
05	7097.0	0.0	0.0	0.0
06	7097.0	0.0	0.0	0.0
07	0.0	0.0	0.0	7097.0
08	0.0	522.0	16.0	6559.0
09	3509.0	610.0	2468.0	510.0
10	1570.75	2584.75	1981.75	959.75
11	2088.0	1712.0	1697.0	1600.0

PFM

	A	C	G	T
01	0.277	0.298	0.251	0.174
02	0.23	0.316	0.372	0.083
03	0.019	0.388	0.182	0.411
04	0.0	0.0	0.0	1.0
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.074	0.002	0.924
09	0.494	0.086	0.348	0.072
10	0.221	0.364	0.279	0.135
11	0.294	0.241	0.239	0.225

PWM

	A	C	G	T
01	0.103	0.176	0.003	-0.363
02	-0.085	0.235	0.396	-1.105
03	-2.568	0.439	-0.316	0.497
04	-6.686	-6.686	-6.686	1.385
05	1.385	-6.686	-6.686	-6.686
06	1.385	-6.686	-6.686	-6.686
07	-6.686	-6.686	-6.686	1.385
08	-6.686	-1.22	-4.58	1.307
09	0.681	-1.065	0.33	-1.244
10	-0.122	0.376	0.11	-0.613
11	0.163	-0.036	-0.044	-0.103

Standard thresholds

P-value	Threshold
0.001	4.563505
0.0005	6.003935
0.0001	7.910445