FOXA3.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA3.H12RSNP.0.PS.A
Gene (human)	FOXA3 (GeneCards)
Gene synonyms (human)	HNF3G, TCF3G
Gene (mouse)	Foxa3
Gene synonyms (mouse)	Hnf3g, Tcf-3g, Tcf3g
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nnTGTTTACWbW
GC content	31.8%
Information content (bits; total / per base)	12.262 / 1.022
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000

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	1 (7)	0.922	0.943	0.848	0.88	0.931	0.948	3.767	3.965	345.638	413.523
Mouse	2 (14)	0.866	0.948	0.809	0.891	0.888	0.956	3.656	4.194	335.879	636.469

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.849	0.847	0.773	0.776	0.651	0.675
Overall, 2 experiments	best	0.996	0.993	0.945	0.942	0.75	0.785
Methyl HT-SELEX, 1 experiments	median	0.703	0.702	0.601	0.609	0.553	0.565
Methyl HT-SELEX, 1 experiments	best	0.703	0.702	0.601	0.609	0.553	0.565
Non-Methyl HT-SELEX, 1 experiments	median	0.996	0.993	0.945	0.942	0.75	0.785
Non-Methyl HT-SELEX, 1 experiments	best	0.996	0.993	0.945	0.942	0.75	0.785

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	100.0	4.933	0.375	0.246

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Fork head/winged helix factors {3.3} (TFClass)
TF family	FOX {3.3.1} (TFClass)
TF subfamily	FOXA {3.3.1.1} (TFClass)
TFClass ID	TFClass: 3.3.1.1.3
HGNC	HGNC:5023
MGI	MGI:1347477
EntrezGene (human)	GeneID:3171 (SSTAR profile)
EntrezGene (mouse)	GeneID:15377 (SSTAR profile)
UniProt ID (human)	FOXA3_HUMAN
UniProt ID (mouse)	FOXA3_MOUSE
UniProt AC (human)	P55318 (TFClass)
UniProt AC (mouse)	P35584 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 2 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	FOXA3.H12RSNP.0.PS.A.pcm
PWM	FOXA3.H12RSNP.0.PS.A.pwm
PFM	FOXA3.H12RSNP.0.PS.A.pfm
Alignment	FOXA3.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	FOXA3.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	FOXA3.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	FOXA3.H12RSNP.0.PS.A_meme_format.meme
Transfac format	FOXA3.H12RSNP.0.PS.A_transfac_format.txt
Homer format	FOXA3.H12RSNP.0.PS.A_homer_format_0.001.txt FOXA3.H12RSNP.0.PS.A_homer_format_0.0005.txt FOXA3.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	235.0	341.0	191.0	233.0
02	288.0	251.0	182.0	279.0
03	7.0	6.0	0.0	987.0
04	214.0	1.0	785.0	0.0
05	1.0	0.0	1.0	998.0
06	1.0	1.0	65.0	933.0
07	1.0	2.0	190.0	807.0
08	806.0	4.0	182.0	8.0
09	0.0	922.0	1.0	77.0
10	405.0	145.0	1.0	449.0
11	89.0	326.0	140.0	445.0
12	493.0	28.0	51.0	428.0

PFM

	A	C	G	T
01	0.235	0.341	0.191	0.233
02	0.288	0.251	0.182	0.279
03	0.007	0.006	0.0	0.987
04	0.214	0.001	0.785	0.0
05	0.001	0.0	0.001	0.998
06	0.001	0.001	0.065	0.933
07	0.001	0.002	0.19	0.807
08	0.806	0.004	0.182	0.008
09	0.0	0.922	0.001	0.077
10	0.405	0.145	0.001	0.449
11	0.089	0.326	0.14	0.445
12	0.493	0.028	0.051	0.428

PWM

	A	C	G	T
01	-0.061	0.309	-0.267	-0.07
02	0.141	0.004	-0.315	0.109
03	-3.362	-3.484	-4.982	1.368
04	-0.154	-4.525	1.14	-4.982
05	-4.525	-4.982	-4.525	1.379
06	-4.525	-4.525	-1.328	1.312
07	-4.525	-4.213	-0.272	1.167
08	1.166	-3.783	-0.315	-3.253
09	-4.982	1.3	-4.525	-1.162
10	0.48	-0.54	-4.525	0.583
11	-1.02	0.264	-0.574	0.574
12	0.676	-2.136	-1.563	0.535

Standard thresholds

P-value	Threshold
0.001	3.69996
0.0005	4.933975
0.0001	7.54059