FOXA1.H12INVIVO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA1.H12INVIVO.1.S.C
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	1
Quality	C

Motif length	16
Consensus	ndWTGTTTACWTARbv
GC content	29.68%
Information content (bits; total / per base)	17.395 / 1.087
Data sources	HT-SELEX
Aligned words	6550

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)	0.895	0.944	0.777	0.883	0.918	0.959	3.442	4.431	219.529	549.456
Mouse	32 (69)	0.89	0.913	0.772	0.82	0.901	0.93	3.379	3.734	369.18	627.149

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.931	0.907	0.803	0.795	0.672	0.687
Overall, 4 experiments	best	0.987	0.986	0.942	0.922	0.837	0.827
Methyl HT-SELEX, 2 experiments	median	0.878	0.844	0.763	0.74	0.659	0.658
Methyl HT-SELEX, 2 experiments	best	0.885	0.852	0.786	0.756	0.684	0.675
Non-Methyl HT-SELEX, 2 experiments	median	0.982	0.974	0.882	0.878	0.748	0.763
Non-Methyl HT-SELEX, 2 experiments	best	0.987	0.986	0.942	0.922	0.837	0.827

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	9.952	181.006	0.326	0.33

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.842	0.271	0.804	0.555
batch 2	0.617	0.349	0.471	0.322

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.1.S.C.pcm
PWM	FOXA1.H12INVIVO.1.S.C.pwm
PFM	FOXA1.H12INVIVO.1.S.C.pfm
Alignment	FOXA1.H12INVIVO.1.S.C.words.tsv
Threshold to P-value map	FOXA1.H12INVIVO.1.S.C.thr
Motif in other formats
JASPAR format	FOXA1.H12INVIVO.1.S.C_jaspar_format.txt
MEME format	FOXA1.H12INVIVO.1.S.C_meme_format.meme
Transfac format	FOXA1.H12INVIVO.1.S.C_transfac_format.txt
Homer format	FOXA1.H12INVIVO.1.S.C_homer_format_0.001.txt FOXA1.H12INVIVO.1.S.C_homer_format_0.0005.txt FOXA1.H12INVIVO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1237.5	1855.5	1914.5	1542.5
02	1942.25	563.25	697.25	3347.25
03	1235.0	366.0	413.0	4536.0
04	6.0	25.0	11.0	6508.0
05	1219.0	3.0	5328.0	0.0
06	0.0	3.0	1.0	6546.0
07	2.0	0.0	10.0	6538.0
08	3.0	2.0	26.0	6519.0
09	6144.0	10.0	396.0	0.0
10	2.0	6213.0	11.0	324.0
11	2470.0	233.0	74.0	3773.0
12	76.0	1183.0	107.0	5184.0
13	5217.0	61.0	134.0	1138.0
14	3205.0	231.0	2684.0	430.0
15	526.0	1846.0	2542.0	1636.0
16	1459.25	1336.25	2822.25	932.25

PFM

	A	C	G	T
01	0.189	0.283	0.292	0.235
02	0.297	0.086	0.106	0.511
03	0.189	0.056	0.063	0.693
04	0.001	0.004	0.002	0.994
05	0.186	0.0	0.813	0.0
06	0.0	0.0	0.0	0.999
07	0.0	0.0	0.002	0.998
08	0.0	0.0	0.004	0.995
09	0.938	0.002	0.06	0.0
10	0.0	0.949	0.002	0.049
11	0.377	0.036	0.011	0.576
12	0.012	0.181	0.016	0.791
13	0.796	0.009	0.02	0.174
14	0.489	0.035	0.41	0.066
15	0.08	0.282	0.388	0.25
16	0.223	0.204	0.431	0.142

PWM

	A	C	G	T
01	-0.28	0.125	0.156	-0.06
02	0.17	-1.065	-0.852	0.714
03	-0.282	-1.494	-1.374	1.018
04	-5.299	-4.099	-4.822	1.379
05	-0.295	-5.754	1.179	-6.615
06	-6.615	-5.754	-6.24	1.385
07	-5.968	-6.615	-4.901	1.383
08	-5.754	-5.968	-4.063	1.381
09	1.321	-4.901	-1.415	-6.615
10	-5.968	1.332	-4.822	-1.615
11	0.411	-1.942	-3.069	0.834
12	-3.043	-0.325	-2.709	1.151
13	1.158	-3.256	-2.488	-0.363
14	0.671	-1.95	0.494	-1.333
15	-1.133	0.12	0.439	-0.001
16	-0.115	-0.203	0.544	-0.562

Standard thresholds

P-value	Threshold
0.001	-0.24499
0.0005	1.47171
0.0001	5.01301