FOXA2.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA2.H12INVIVO.1.SM.B
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	1
Quality	B

Motif length	16
Consensus	nvYMAATATTTAChhn
GC content	31.28%
Information content (bits; total / per base)	15.872 / 0.992
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	967

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)	0.803	0.871	0.628	0.737	0.8	0.888	2.512	3.143	88.854	233.041
Mouse	20 (114)	0.795	0.86	0.62	0.722	0.755	0.856	2.222	3.162	102.639	212.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.982	0.975	0.953	0.937	0.889	0.869
Overall, 2 experiments	best	0.993	0.991	0.965	0.955	0.889	0.878
Methyl HT-SELEX, 1 experiments	median	0.993	0.991	0.965	0.955	0.889	0.878
Methyl HT-SELEX, 1 experiments	best	0.993	0.991	0.965	0.955	0.889	0.878
Non-Methyl HT-SELEX, 1 experiments	median	0.972	0.96	0.942	0.919	0.888	0.861
Non-Methyl HT-SELEX, 1 experiments	best	0.972	0.96	0.942	0.919	0.888	0.861

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.142	18.881	0.226	0.202

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.915	0.441	0.903	0.547
batch 2	0.672	0.069	0.781	0.559

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.H12INVIVO.1.SM.B.pcm
PWM	FOXA2.H12INVIVO.1.SM.B.pwm
PFM	FOXA2.H12INVIVO.1.SM.B.pfm
Alignment	FOXA2.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	FOXA2.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	FOXA2.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	FOXA2.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	FOXA2.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	FOXA2.H12INVIVO.1.SM.B_homer_format_0.001.txt FOXA2.H12INVIVO.1.SM.B_homer_format_0.0005.txt FOXA2.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	230.25	213.25	225.25	298.25
02	202.25	118.25	529.25	117.25
03	41.0	307.0	60.0	559.0
04	371.0	479.0	65.0	52.0
05	805.0	54.0	25.0	83.0
06	869.0	13.0	9.0	76.0
07	0.0	0.0	0.0	967.0
08	779.0	0.0	188.0	0.0
09	0.0	0.0	0.0	967.0
10	0.0	0.0	0.0	967.0
11	0.0	0.0	127.0	840.0
12	656.0	0.0	311.0	0.0
13	6.0	911.0	2.0	48.0
14	286.0	231.0	120.0	330.0
15	92.5	442.5	77.5	354.5
16	311.5	148.5	182.5	324.5

PFM

	A	C	G	T
01	0.238	0.221	0.233	0.308
02	0.209	0.122	0.547	0.121
03	0.042	0.317	0.062	0.578
04	0.384	0.495	0.067	0.054
05	0.832	0.056	0.026	0.086
06	0.899	0.013	0.009	0.079
07	0.0	0.0	0.0	1.0
08	0.806	0.0	0.194	0.0
09	0.0	0.0	0.0	1.0
10	0.0	0.0	0.0	1.0
11	0.0	0.0	0.131	0.869
12	0.678	0.0	0.322	0.0
13	0.006	0.942	0.002	0.05
14	0.296	0.239	0.124	0.341
15	0.096	0.458	0.08	0.367
16	0.322	0.154	0.189	0.336

PWM

	A	C	G	T
01	-0.048	-0.124	-0.07	0.209
02	-0.177	-0.708	0.78	-0.716
03	-1.74	0.237	-1.372	0.834
04	0.426	0.68	-1.295	-1.511
05	1.198	-1.475	-2.21	-1.056
06	1.274	-2.806	-3.123	-1.142
07	-4.954	-4.954	-4.954	1.381
08	1.165	-4.954	-0.249	-4.954
09	-4.954	-4.954	-4.954	1.381
10	-4.954	-4.954	-4.954	1.381
11	-4.954	-4.954	-0.637	1.24
12	0.994	-4.954	0.25	-4.954
13	-3.451	1.321	-4.182	-1.589
14	0.167	-0.045	-0.693	0.309
15	-0.949	0.601	-1.123	0.381
16	0.252	-0.483	-0.279	0.293

Standard thresholds

P-value	Threshold
0.001	1.72306
0.0005	3.18311
0.0001	6.19371