PHX2B.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PHX2B.H12INVIVO.0.PSM.A
Gene (human)	PHOX2B (GeneCards)
Gene synonyms (human)	PMX2B
Gene (mouse)	Phox2b
Gene synonyms (mouse)	Pmx2b
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	TAATTARATTAd
GC content	8.39%
Information content (bits; total / per base)	16.727 / 1.394
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1004

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)	0.923	0.975	0.851	0.949	0.841	0.949	3.033	4.625	249.26	431.292

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.986	0.974	0.974	0.962	0.852	0.836
Overall, 8 experiments	best	1.0	0.999	0.999	0.999	0.994	0.993
Methyl HT-SELEX, 2 experiments	median	0.95	0.918	0.926	0.895	0.783	0.784
Methyl HT-SELEX, 2 experiments	best	1.0	0.999	0.977	0.977	0.824	0.799
Non-Methyl HT-SELEX, 6 experiments	median	0.986	0.974	0.976	0.962	0.923	0.911
Non-Methyl HT-SELEX, 6 experiments	best	0.999	0.999	0.999	0.999	0.994	0.993

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.H12INVIVO.0.PSM.A.pcm
PWM	PHX2B.H12INVIVO.0.PSM.A.pwm
PFM	PHX2B.H12INVIVO.0.PSM.A.pfm
Alignment	PHX2B.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	PHX2B.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	PHX2B.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	PHX2B.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	PHX2B.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	PHX2B.H12INVIVO.0.PSM.A_homer_format_0.001.txt PHX2B.H12INVIVO.0.PSM.A_homer_format_0.0005.txt PHX2B.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	46.0	12.0	8.0	938.0
02	966.0	2.0	25.0	11.0
03	1002.0	0.0	2.0	0.0
04	5.0	6.0	7.0	986.0
05	8.0	65.0	26.0	905.0
06	813.0	0.0	191.0	0.0
07	689.0	57.0	225.0	33.0
08	863.0	25.0	52.0	64.0
09	4.0	4.0	3.0	993.0
10	60.0	31.0	14.0	899.0
11	886.0	4.0	22.0	92.0
12	527.0	105.0	125.0	247.0

PFM

	A	C	G	T
01	0.046	0.012	0.008	0.934
02	0.962	0.002	0.025	0.011
03	0.998	0.0	0.002	0.0
04	0.005	0.006	0.007	0.982
05	0.008	0.065	0.026	0.901
06	0.81	0.0	0.19	0.0
07	0.686	0.057	0.224	0.033
08	0.86	0.025	0.052	0.064
09	0.004	0.004	0.003	0.989
10	0.06	0.031	0.014	0.895
11	0.882	0.004	0.022	0.092
12	0.525	0.105	0.125	0.246

PWM

	A	C	G	T
01	-1.667	-2.913	-3.257	1.313
02	1.343	-4.216	-2.247	-2.989
03	1.379	-4.985	-4.216	-4.985
04	-3.626	-3.487	-3.366	1.363
05	-3.257	-1.332	-2.21	1.278
06	1.171	-4.985	-0.271	-4.985
07	1.005	-1.459	-0.109	-1.985
08	1.23	-2.247	-1.548	-1.347
09	-3.787	-3.787	-3.979	1.37
10	-1.41	-2.044	-2.777	1.271
11	1.256	-3.787	-2.366	-0.992
12	0.738	-0.862	-0.69	-0.016

Standard thresholds

P-value	Threshold
0.001	1.773135
0.0005	3.11493
0.0001	5.91484