FOXA1.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA1.H12INVIVO.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	12
Consensus	TRTTTACWbWdn
GC content	33.08%
Information content (bits; total / per base)	10.997 / 0.916
Data sources	ChIP-Seq
Aligned words	952

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)	0.931	0.97	0.856	0.933	0.937	0.968	3.764	4.481	278.355	723.337
Mouse	32 (69)	0.933	0.952	0.863	0.899	0.941	0.955	3.902	4.214	478.824	738.051

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.931	0.906	0.802	0.793	0.669	0.685
Overall, 4 experiments	best	0.986	0.983	0.952	0.933	0.854	0.843
Methyl HT-SELEX, 2 experiments	median	0.874	0.838	0.758	0.735	0.654	0.654
Methyl HT-SELEX, 2 experiments	best	0.882	0.846	0.781	0.751	0.677	0.67
Non-Methyl HT-SELEX, 2 experiments	median	0.983	0.975	0.888	0.884	0.757	0.772
Non-Methyl HT-SELEX, 2 experiments	best	0.986	0.983	0.952	0.933	0.854	0.843

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	10.38	185.239	0.352	0.341

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.849	0.312	0.867	0.651
batch 2	0.738	0.434	0.701	0.523

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.H12INVIVO.0.P.B.pcm
PWM	FOXA1.H12INVIVO.0.P.B.pwm
PFM	FOXA1.H12INVIVO.0.P.B.pfm
Alignment	FOXA1.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	FOXA1.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	FOXA1.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	FOXA1.H12INVIVO.0.P.B_meme_format.meme
Transfac format	FOXA1.H12INVIVO.0.P.B_transfac_format.txt
Homer format	FOXA1.H12INVIVO.0.P.B_homer_format_0.001.txt FOXA1.H12INVIVO.0.P.B_homer_format_0.0005.txt FOXA1.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	29.0	12.0	17.0	894.0
02	308.0	16.0	621.0	7.0
03	8.0	12.0	8.0	924.0
04	11.0	0.0	69.0	872.0
05	7.0	5.0	146.0	794.0
06	794.0	8.0	136.0	14.0
07	14.0	814.0	11.0	113.0
08	390.0	149.0	9.0	404.0
09	72.0	323.0	138.0	419.0
10	423.0	44.0	72.0	413.0
11	188.0	163.0	427.0	174.0
12	114.0	306.0	273.0	259.0

PFM

	A	C	G	T
01	0.03	0.013	0.018	0.939
02	0.324	0.017	0.652	0.007
03	0.008	0.013	0.008	0.971
04	0.012	0.0	0.072	0.916
05	0.007	0.005	0.153	0.834
06	0.834	0.008	0.143	0.015
07	0.015	0.855	0.012	0.119
08	0.41	0.157	0.009	0.424
09	0.076	0.339	0.145	0.44
10	0.444	0.046	0.076	0.434
11	0.197	0.171	0.449	0.183
12	0.12	0.321	0.287	0.272

PWM

	A	C	G	T
01	-2.055	-2.861	-2.55	1.318
02	0.256	-2.605	0.955	-3.314
03	-3.206	-2.861	-3.206	1.351
04	-2.937	-4.94	-1.221	1.293
05	-3.314	-3.575	-0.484	1.2
06	1.2	-3.206	-0.554	-2.725
07	-2.725	1.225	-2.937	-0.737
08	0.491	-0.464	-3.108	0.526
09	-1.179	0.303	-0.54	0.563
10	0.572	-1.657	-1.179	0.548
11	-0.234	-0.375	0.581	-0.311
12	-0.728	0.25	0.136	0.084

Standard thresholds

P-value	Threshold
0.001	4.47436
0.0005	5.430525
0.0001	7.3627