FOXA2.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA2.H12CORE.0.PSM.A
Gene (human)	FOXA2 (GeneCards)
Gene synonyms (human)	HNF3B, TCF3B
Gene (mouse)	Foxa2
Gene synonyms (mouse)	Hnf3b, Tcf-3b, Tcf3b
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	TGTTTACWbWdn
GC content	33.1%
Information content (bits; total / per base)	13.023 / 1.085
Data sources	ChIP-Seq + HT-SELEX + Methyl-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	54 (310)	0.918	0.973	0.85	0.954	0.923	0.974	3.664	5.074	263.436	623.268
Mouse	20 (114)	0.9	0.961	0.838	0.921	0.904	0.963	3.634	4.418	280.404	573.398

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.981	0.966	0.967	0.949	0.926	0.904
Overall, 2 experiments	best	0.988	0.979	0.977	0.964	0.93	0.915
Methyl HT-SELEX, 1 experiments	median	0.988	0.979	0.977	0.964	0.93	0.915
Methyl HT-SELEX, 1 experiments	best	0.988	0.979	0.977	0.964	0.93	0.915
Non-Methyl HT-SELEX, 1 experiments	median	0.973	0.953	0.958	0.934	0.921	0.893
Non-Methyl HT-SELEX, 1 experiments	best	0.973	0.953	0.958	0.934	0.921	0.893

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	13.819	47.484	0.325	0.284

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.965	0.785	0.923	0.472
batch 2	0.679	0.097	0.675	0.476

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: 3.3.1.1.2
HGNC	HGNC:5022
MGI	MGI:1347476
EntrezGene (human)	GeneID:3170 (SSTAR profile)
EntrezGene (mouse)	GeneID:15376 (SSTAR profile)
UniProt ID (human)	FOXA2_HUMAN
UniProt ID (mouse)	FOXA2_MOUSE
UniProt AC (human)	Q9Y261 (TFClass)
UniProt AC (mouse)	P35583 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	54 human, 20 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	FOXA2.H12CORE.0.PSM.A.pcm
PWM	FOXA2.H12CORE.0.PSM.A.pwm
PFM	FOXA2.H12CORE.0.PSM.A.pfm
Alignment	FOXA2.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	FOXA2.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	FOXA2.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	FOXA2.H12CORE.0.PSM.A_meme_format.meme
Transfac format	FOXA2.H12CORE.0.PSM.A_transfac_format.txt
Homer format	FOXA2.H12CORE.0.PSM.A_homer_format_0.001.txt FOXA2.H12CORE.0.PSM.A_homer_format_0.0005.txt FOXA2.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	8.0	4.0	1.0	987.0
02	265.0	1.0	734.0	0.0
03	0.0	1.0	1.0	998.0
04	0.0	0.0	63.0	937.0
05	2.0	0.0	215.0	783.0
06	823.0	1.0	175.0	1.0
07	7.0	947.0	0.0	46.0
08	442.0	115.0	2.0	441.0
09	61.0	378.0	87.0	474.0
10	601.0	6.0	22.0	371.0
11	229.0	112.0	482.0	177.0
12	129.0	280.0	345.0	246.0

PFM

	A	C	G	T
01	0.008	0.004	0.001	0.987
02	0.265	0.001	0.734	0.0
03	0.0	0.001	0.001	0.998
04	0.0	0.0	0.063	0.937
05	0.002	0.0	0.215	0.783
06	0.823	0.001	0.175	0.001
07	0.007	0.947	0.0	0.046
08	0.442	0.115	0.002	0.441
09	0.061	0.378	0.087	0.474
10	0.601	0.006	0.022	0.371
11	0.229	0.112	0.482	0.177
12	0.129	0.28	0.345	0.246

PWM

	A	C	G	T
01	-3.253	-3.783	-4.525	1.368
02	0.058	-4.525	1.073	-4.982
03	-4.982	-4.525	-4.525	1.379
04	-4.982	-4.982	-1.358	1.316
05	-4.213	-4.982	-0.15	1.137
06	1.187	-4.525	-0.354	-4.525
07	-3.362	1.327	-4.982	-1.663
08	0.567	-0.769	-4.213	0.565
09	-1.39	0.411	-1.043	0.636
10	0.873	-3.484	-2.362	0.393
11	-0.087	-0.795	0.653	-0.342
12	-0.655	0.113	0.32	-0.016

Standard thresholds

P-value	Threshold
0.001	3.312975
0.0005	4.533515
0.0001	7.280665