FOXA2.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXA2.H12INVITRO.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	nnhdTRTTTAYhhd
GC content	33.13%
Information content (bits; total / per base)	10.779 / 0.77
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9919

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)	0.869	0.939	0.732	0.859	0.899	0.941	3.177	3.88	212.523	547.796
Mouse	20 (114)	0.848	0.91	0.707	0.802	0.865	0.929	2.954	3.564	225.546	484.027

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.984	0.975	0.97	0.955	0.923	0.905
Overall, 2 experiments	best	0.993	0.99	0.98	0.972	0.927	0.915
Methyl HT-SELEX, 1 experiments	median	0.993	0.99	0.98	0.972	0.927	0.915
Methyl HT-SELEX, 1 experiments	best	0.993	0.99	0.98	0.972	0.927	0.915
Non-Methyl HT-SELEX, 1 experiments	median	0.976	0.959	0.96	0.939	0.92	0.895
Non-Methyl HT-SELEX, 1 experiments	best	0.976	0.959	0.96	0.939	0.92	0.895

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.655	26.165	0.264	0.238

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.958	0.619	0.897	0.46
batch 2	0.7	0.067	0.631	0.513

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.H12INVITRO.0.PSM.A.pcm
PWM	FOXA2.H12INVITRO.0.PSM.A.pwm
PFM	FOXA2.H12INVITRO.0.PSM.A.pfm
Alignment	FOXA2.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	FOXA2.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	FOXA2.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	FOXA2.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	FOXA2.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	FOXA2.H12INVITRO.0.PSM.A_homer_format_0.001.txt FOXA2.H12INVITRO.0.PSM.A_homer_format_0.0005.txt FOXA2.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1767.0	2702.0	1961.0	3489.0
02	2565.75	3189.75	2315.75	1847.75
03	4002.0	1916.0	1434.0	2567.0
04	4682.0	1376.0	1510.0	2351.0
05	21.0	172.0	62.0	9664.0
06	5166.0	29.0	4722.0	2.0
07	0.0	4.0	0.0	9915.0
08	0.0	0.0	132.0	9787.0
09	10.0	5.0	1574.0	8330.0
10	6324.0	21.0	3562.0	12.0
11	514.0	7719.0	226.0	1460.0
12	3152.0	2190.0	1285.0	3292.0
13	1223.5	3652.5	1166.5	3876.5
14	3582.25	1326.25	1747.25	3263.25

PFM

	A	C	G	T
01	0.178	0.272	0.198	0.352
02	0.259	0.322	0.233	0.186
03	0.403	0.193	0.145	0.259
04	0.472	0.139	0.152	0.237
05	0.002	0.017	0.006	0.974
06	0.521	0.003	0.476	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.013	0.987
09	0.001	0.001	0.159	0.84
10	0.638	0.002	0.359	0.001
11	0.052	0.778	0.023	0.147
12	0.318	0.221	0.13	0.332
13	0.123	0.368	0.118	0.391
14	0.361	0.134	0.176	0.329

PWM

	A	C	G	T
01	-0.339	0.086	-0.234	0.341
02	0.034	0.252	-0.068	-0.294
03	0.478	-0.258	-0.547	0.035
04	0.635	-0.588	-0.495	-0.053
05	-4.668	-2.656	-3.653	1.36
06	0.733	-4.373	0.644	-6.358
07	-6.984	-5.976	-6.984	1.385
08	-6.984	-6.984	-2.917	1.372
09	-5.307	-5.829	-0.454	1.211
10	0.936	-4.668	0.362	-5.157
11	-1.57	1.135	-2.386	-0.529
12	0.24	-0.124	-0.657	0.283
13	-0.705	0.387	-0.753	0.446
14	0.368	-0.625	-0.35	0.274

Standard thresholds

P-value	Threshold
0.001	4.48651
0.0005	5.73001
0.0001	7.67466