FOXA2.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA2.H12RSNP.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	11
Consensus	TGTTTACWhWn
GC content	30.95%
Information content (bits; total / per base)	12.141 / 1.104
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)	0.916	0.968	0.842	0.933	0.925	0.969	3.617	4.846	256.617	601.222
Mouse	20 (114)	0.894	0.954	0.823	0.901	0.902	0.957	3.508	4.199	270.998	564.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.978	0.962	0.965	0.945	0.924	0.901
Overall, 2 experiments	best	0.986	0.975	0.975	0.96	0.929	0.912
Methyl HT-SELEX, 1 experiments	median	0.986	0.975	0.975	0.96	0.929	0.912
Methyl HT-SELEX, 1 experiments	best	0.986	0.975	0.975	0.96	0.929	0.912
Non-Methyl HT-SELEX, 1 experiments	median	0.97	0.948	0.956	0.929	0.919	0.89
Non-Methyl HT-SELEX, 1 experiments	best	0.97	0.948	0.956	0.929	0.919	0.89

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	9.211	37.141	0.301	0.258

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.969	0.707	0.927	0.506
batch 2	0.764	0.129	0.687	0.497

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.H12RSNP.0.PSM.A.pcm
PWM	FOXA2.H12RSNP.0.PSM.A.pwm
PFM	FOXA2.H12RSNP.0.PSM.A.pfm
Alignment	FOXA2.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	FOXA2.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	FOXA2.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	FOXA2.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	FOXA2.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	FOXA2.H12RSNP.0.PSM.A_homer_format_0.001.txt FOXA2.H12RSNP.0.PSM.A_homer_format_0.0005.txt FOXA2.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	9.0	7.0	3.0	981.0
02	213.0	1.0	786.0	0.0
03	8.0	0.0	1.0	991.0
04	1.0	0.0	22.0	977.0
05	0.0	0.0	177.0	823.0
06	762.0	12.0	222.0	4.0
07	10.0	902.0	1.0	87.0
08	403.0	159.0	10.0	428.0
09	106.0	330.0	103.0	461.0
10	492.0	27.0	58.0	423.0
11	210.0	205.0	378.0	207.0

PFM

	A	C	G	T
01	0.009	0.007	0.003	0.981
02	0.213	0.001	0.786	0.0
03	0.008	0.0	0.001	0.991
04	0.001	0.0	0.022	0.977
05	0.0	0.0	0.177	0.823
06	0.762	0.012	0.222	0.004
07	0.01	0.902	0.001	0.087
08	0.403	0.159	0.01	0.428
09	0.106	0.33	0.103	0.461
10	0.492	0.027	0.058	0.423
11	0.21	0.205	0.378	0.207

PWM

	A	C	G	T
01	-3.156	-3.362	-3.975	1.362
02	-0.159	-4.525	1.141	-4.982
03	-3.253	-4.982	-4.525	1.372
04	-4.525	-4.982	-2.362	1.358
05	-4.982	-4.982	-0.342	1.187
06	1.11	-2.909	-0.118	-3.783
07	-3.066	1.278	-4.525	-1.043
08	0.475	-0.449	-3.066	0.535
09	-0.849	0.276	-0.877	0.609
10	0.674	-2.171	-1.439	0.523
11	-0.173	-0.197	0.411	-0.187

Standard thresholds

P-value	Threshold
0.001	3.841955
0.0005	4.98286
0.0001	7.520475