FOXA2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA2.H12INVIVO.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	14
Consensus	bbbTGTTTACWbWv
GC content	36.79%
Information content (bits; total / per base)	12.954 / 0.925
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	982

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)	0.926	0.975	0.86	0.957	0.927	0.975	3.732	5.188	273.527	673.553
Mouse	20 (114)	0.904	0.963	0.844	0.926	0.912	0.963	3.775	4.536	290.039	650.678

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.977	0.961	0.962	0.941	0.916	0.892
Overall, 2 experiments	best	0.984	0.973	0.97	0.954	0.917	0.899
Methyl HT-SELEX, 1 experiments	median	0.984	0.973	0.97	0.954	0.917	0.899
Methyl HT-SELEX, 1 experiments	best	0.984	0.973	0.97	0.954	0.917	0.899
Non-Methyl HT-SELEX, 1 experiments	median	0.97	0.949	0.954	0.929	0.914	0.885
Non-Methyl HT-SELEX, 1 experiments	best	0.97	0.949	0.954	0.929	0.914	0.885

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	9.975	39.658	0.317	0.272

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.927	0.691	0.864	0.471
batch 2	0.667	0.097	0.486	0.298

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.0.PSM.A.pcm
PWM	FOXA2.H12INVIVO.0.PSM.A.pwm
PFM	FOXA2.H12INVIVO.0.PSM.A.pfm
Alignment	FOXA2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	FOXA2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	FOXA2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	FOXA2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	FOXA2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	FOXA2.H12INVIVO.0.PSM.A_homer_format_0.001.txt FOXA2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt FOXA2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	130.0	417.0	219.0	216.0
02	126.0	377.0	234.0	245.0
03	132.0	259.0	223.0	368.0
04	11.0	1.0	5.0	965.0
05	204.0	6.0	772.0	0.0
06	5.0	3.0	2.0	972.0
07	2.0	0.0	44.0	936.0
08	0.0	0.0	226.0	756.0
09	871.0	5.0	98.0	8.0
10	3.0	907.0	1.0	71.0
11	424.0	128.0	9.0	421.0
12	66.0	344.0	100.0	472.0
13	541.0	24.0	40.0	377.0
14	229.0	150.0	464.0	139.0

PFM

	A	C	G	T
01	0.132	0.425	0.223	0.22
02	0.128	0.384	0.238	0.249
03	0.134	0.264	0.227	0.375
04	0.011	0.001	0.005	0.983
05	0.208	0.006	0.786	0.0
06	0.005	0.003	0.002	0.99
07	0.002	0.0	0.045	0.953
08	0.0	0.0	0.23	0.77
09	0.887	0.005	0.1	0.008
10	0.003	0.924	0.001	0.072
11	0.432	0.13	0.009	0.429
12	0.067	0.35	0.102	0.481
13	0.551	0.024	0.041	0.384
14	0.233	0.153	0.473	0.142

PWM

	A	C	G	T
01	-0.63	0.527	-0.113	-0.127
02	-0.66	0.427	-0.048	-0.002
03	-0.615	0.053	-0.095	0.402
04	-2.967	-4.509	-3.605	1.364
05	-0.184	-3.466	1.141	-4.967
06	-3.605	-3.958	-4.196	1.371
07	-4.196	-4.967	-1.688	1.333
08	-4.967	-4.967	-0.082	1.12
09	1.261	-3.605	-0.908	-3.236
10	-3.958	1.302	-4.509	-1.224
11	0.543	-0.645	-3.138	0.536
12	-1.295	0.335	-0.888	0.65
13	0.786	-2.263	-1.779	0.427
14	-0.069	-0.488	0.633	-0.563

Standard thresholds

P-value	Threshold
0.001	3.55186
0.0005	4.72001
0.0001	7.18536