PHX2B.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PHX2B.H12INVITRO.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	14
Consensus	nnTAATTARATTAn
GC content	18.36%
Information content (bits; total / per base)	18.86 / 1.347
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8849

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)	0.934	0.974	0.871	0.949	0.842	0.937	2.952	4.538	240.377	386.276

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.99	0.982	0.977	0.971	0.859	0.843
Overall, 8 experiments	best	1.0	1.0	1.0	0.999	0.995	0.995
Methyl HT-SELEX, 2 experiments	median	0.956	0.929	0.932	0.904	0.794	0.795
Methyl HT-SELEX, 2 experiments	best	1.0	0.999	0.979	0.978	0.834	0.806
Non-Methyl HT-SELEX, 6 experiments	median	0.99	0.982	0.981	0.971	0.927	0.92
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	1.0	0.999	0.995	0.995

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.H12INVITRO.0.PSM.A.pcm
PWM	PHX2B.H12INVITRO.0.PSM.A.pwm
PFM	PHX2B.H12INVITRO.0.PSM.A.pfm
Alignment	PHX2B.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	PHX2B.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	PHX2B.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	PHX2B.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	PHX2B.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	PHX2B.H12INVITRO.0.PSM.A_homer_format_0.001.txt PHX2B.H12INVITRO.0.PSM.A_homer_format_0.0005.txt PHX2B.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1818.75	2334.75	3107.75	1587.75
02	1683.25	3092.25	1713.25	2360.25
03	168.0	81.0	15.0	8585.0
04	8749.0	5.0	86.0	9.0
05	8847.0	2.0	0.0	0.0
06	0.0	3.0	0.0	8846.0
07	2.0	27.0	14.0	8806.0
08	7372.0	132.0	1181.0	164.0
09	3590.0	234.0	5020.0	5.0
10	8394.0	47.0	351.0	57.0
11	3.0	6.0	19.0	8821.0
12	67.0	185.0	43.0	8554.0
13	8443.0	49.0	107.0	250.0
14	2315.0	1749.0	3136.0	1649.0

PFM

	A	C	G	T
01	0.206	0.264	0.351	0.179
02	0.19	0.349	0.194	0.267
03	0.019	0.009	0.002	0.97
04	0.989	0.001	0.01	0.001
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.003	0.002	0.995
08	0.833	0.015	0.133	0.019
09	0.406	0.026	0.567	0.001
10	0.949	0.005	0.04	0.006
11	0.0	0.001	0.002	0.997
12	0.008	0.021	0.005	0.967
13	0.954	0.006	0.012	0.028
14	0.262	0.198	0.354	0.186

PWM

	A	C	G	T
01	-0.196	0.054	0.34	-0.331
02	-0.273	0.335	-0.255	0.065
03	-2.565	-3.281	-4.854	1.355
04	1.374	-5.719	-3.222	-5.28
05	1.385	-6.251	-6.882	-6.882
06	-6.882	-6.04	-6.882	1.385
07	-6.251	-4.326	-4.913	1.381
08	1.203	-2.803	-0.627	-2.589
09	0.484	-2.238	0.819	-5.719
10	1.333	-3.805	-1.836	-3.621
11	-6.04	-5.59	-4.645	1.382
12	-3.465	-2.47	-3.89	1.352
13	1.339	-3.766	-3.009	-2.172
14	0.045	-0.235	0.349	-0.293

Standard thresholds

P-value	Threshold
0.001	-1.90169
0.0005	-0.08094
0.0001	3.74221