FOXA1.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA1.H12RSNP.0.P.B
Gene (human)	FOXA1 (GeneCards)
Gene synonyms (human)	HNF3A, TCF3A
Gene (mouse)	Foxa1
Gene synonyms (mouse)	Hnf3a, Tcf-3a, Tcf3a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	TGTTTACWbdv
GC content	31.27%
Information content (bits; total / per base)	10.072 / 0.916
Data sources	ChIP-Seq
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	203 (408)	0.93	0.969	0.854	0.932	0.935	0.964	3.651	4.327	276.431	728.086
Mouse	32 (69)	0.93	0.946	0.857	0.887	0.936	0.949	3.754	4.028	474.081	723.137

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.933	0.908	0.811	0.799	0.677	0.691
Overall, 4 experiments	best	0.986	0.983	0.954	0.934	0.859	0.847
Methyl HT-SELEX, 2 experiments	median	0.879	0.843	0.768	0.742	0.662	0.66
Methyl HT-SELEX, 2 experiments	best	0.886	0.851	0.791	0.759	0.686	0.677
Non-Methyl HT-SELEX, 2 experiments	median	0.982	0.974	0.892	0.887	0.763	0.776
Non-Methyl HT-SELEX, 2 experiments	best	0.986	0.983	0.954	0.934	0.859	0.847

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	8.24	158.291	0.333	0.321

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.917	0.259	0.893	0.668
batch 2	0.792	0.481	0.67	0.496

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: 3.3.1.1.1
HGNC	HGNC:5021
MGI	MGI:1347472
EntrezGene (human)	GeneID:3169 (SSTAR profile)
EntrezGene (mouse)	GeneID:15375 (SSTAR profile)
UniProt ID (human)	FOXA1_HUMAN
UniProt ID (mouse)	FOXA1_MOUSE
UniProt AC (human)	P55317 (TFClass)
UniProt AC (mouse)	P35582 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	203 human, 32 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	FOXA1.H12RSNP.0.P.B.pcm
PWM	FOXA1.H12RSNP.0.P.B.pwm
PFM	FOXA1.H12RSNP.0.P.B.pfm
Alignment	FOXA1.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	FOXA1.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	FOXA1.H12RSNP.0.P.B_jaspar_format.txt
MEME format	FOXA1.H12RSNP.0.P.B_meme_format.meme
Transfac format	FOXA1.H12RSNP.0.P.B_transfac_format.txt
Homer format	FOXA1.H12RSNP.0.P.B_homer_format_0.001.txt FOXA1.H12RSNP.0.P.B_homer_format_0.0005.txt FOXA1.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	32.0	17.0	23.0	932.0
02	272.0	10.0	716.0	6.0
03	9.0	20.0	25.0	950.0
04	11.0	4.0	99.0	890.0
05	6.0	3.0	178.0	817.0
06	773.0	10.0	193.0	28.0
07	30.0	805.0	13.0	156.0
08	414.0	150.0	23.0	417.0
09	108.0	273.0	166.0	457.0
10	477.0	65.0	81.0	381.0
11	250.0	180.0	400.0	174.0

PFM

	A	C	G	T
01	0.032	0.017	0.023	0.928
02	0.271	0.01	0.713	0.006
03	0.009	0.02	0.025	0.946
04	0.011	0.004	0.099	0.886
05	0.006	0.003	0.177	0.814
06	0.77	0.01	0.192	0.028
07	0.03	0.802	0.013	0.155
08	0.412	0.149	0.023	0.415
09	0.108	0.272	0.165	0.455
10	0.475	0.065	0.081	0.379
11	0.249	0.179	0.398	0.173

PWM

	A	C	G	T
01	-2.014	-2.602	-2.324	1.307
02	0.08	-3.07	1.044	-3.487
03	-3.159	-2.454	-2.247	1.326
04	-2.989	-3.787	-0.92	1.261
05	-3.487	-3.979	-0.341	1.175
06	1.12	-3.07	-0.261	-2.14
07	-2.075	1.161	-2.843	-0.471
08	0.498	-0.51	-2.324	0.505
09	-0.834	0.083	-0.41	0.596
10	0.639	-1.332	-1.117	0.415
11	-0.004	-0.33	0.463	-0.363

Standard thresholds

P-value	Threshold
0.001	4.71108
0.0005	5.581055
0.0001	7.38965