PHX2B.H14INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PHX2B.H14INVITRO.1.SM.B
Gene (human)	PHOX2B (GeneCards)
Gene synonyms (human)	PMX2B
Gene (mouse)	Phox2b
Gene synonyms (mouse)	Pmx2b
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	11
Consensus	nvbTAATYvvn
GC content	37.02%
Information content (bits; total / per base)	9.46 / 0.86
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8974
Previous names	PHX2B.H12INVITRO.1.SM.B

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)	0.874	0.946	0.768	0.891	0.658	0.743	1.506	1.787	54.481	87.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.953	0.922	0.914	0.88	0.847	0.806
Overall, 8 experiments	best	0.975	0.958	0.969	0.945	0.941	0.915
Methyl HT-SELEX, 2 experiments	median	0.94	0.9	0.904	0.862	0.806	0.784
Methyl HT-SELEX, 2 experiments	best	0.958	0.926	0.913	0.881	0.852	0.801
Non-Methyl HT-SELEX, 6 experiments	median	0.956	0.928	0.931	0.898	0.878	0.845
Non-Methyl HT-SELEX, 6 experiments	best	0.975	0.958	0.969	0.945	0.941	0.915

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	PHX2B.H14INVITRO.1.SM.B.pcm
PWM	PHX2B.H14INVITRO.1.SM.B.pwm
PFM	PHX2B.H14INVITRO.1.SM.B.pfm
Threshold to P-value map	PHX2B.H14INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	PHX2B.H14INVITRO.1.SM.B_jaspar_format.txt
MEME format	PHX2B.H14INVITRO.1.SM.B_meme_format.meme
Transfac format	PHX2B.H14INVITRO.1.SM.B_transfac_format.txt
Homer format	PHX2B.H14INVITRO.1.SM.B_homer_format_0.001.txt PHX2B.H14INVITRO.1.SM.B_homer_format_0.0005.txt PHX2B.H14INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2387.25	2730.25	2279.25	1577.25
02	1795.0	2773.0	3721.0	685.0
03	299.0	3958.0	2078.0	2639.0
04	0.0	0.0	0.0	8974.0
05	8974.0	0.0	0.0	0.0
06	8974.0	0.0	0.0	0.0
07	0.0	10.0	0.0	8964.0
08	89.0	2398.0	1475.0	5012.0
09	4076.0	1114.0	3140.0	644.0
10	1773.5	3210.5	2790.5	1199.5
11	2119.5	2263.5	2599.5	1991.5

PFM

	A	C	G	T
01	0.266	0.304	0.254	0.176
02	0.2	0.309	0.415	0.076
03	0.033	0.441	0.232	0.294
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	0.001	0.0	0.999
08	0.01	0.267	0.164	0.559
09	0.454	0.124	0.35	0.072
10	0.198	0.358	0.311	0.134
11	0.236	0.252	0.29	0.222

PWM

	A	C	G	T
01	0.062	0.196	0.016	-0.352
02	-0.223	0.212	0.506	-1.184
03	-2.009	0.567	-0.077	0.162
04	-6.895	-6.895	-6.895	1.386
05	1.386	-6.895	-6.895	-6.895
06	1.386	-6.895	-6.895	-6.895
07	-6.895	-5.209	-6.895	1.384
08	-3.203	0.067	-0.419	0.803
09	0.597	-0.699	0.336	-1.246
10	-0.235	0.358	0.218	-0.625
11	-0.057	0.009	0.147	-0.119

Standard thresholds

P-value	Threshold
0.001	5.58343
0.0005	6.356335
0.0001	7.41234