HNF4A.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HNF4A.H12INVIVO.0.PSM.A
Gene (human)	HNF4A (GeneCards)
Gene synonyms (human)	HNF4, NR2A1, TCF14
Gene (mouse)	Hnf4a
Gene synonyms (mouse)	Hnf-4, Hnf4, Nr2a1, Tcf14
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	14
Consensus	vRGdnCAAAGTYCW
GC content	50.23%
Information content (bits; total / per base)	14.247 / 1.018
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	26 (169)	0.955	0.987	0.916	0.97	0.936	0.979	4.36	5.402	366.538	627.237
Mouse	25 (165)	0.942	0.972	0.884	0.942	0.92	0.957	3.692	4.503	329.409	472.377

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.882	0.887	0.684	0.712	0.586	0.621
Overall, 7 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.917	0.925	0.719	0.763
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.917	0.925	0.719	0.763
Non-Methyl HT-SELEX, 6 experiments	median	0.787	0.802	0.627	0.658	0.56	0.588
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	9.449	26.983	0.414	0.351

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	RXR-related receptors {2.1.3} (TFClass)
TF subfamily	HNF4 (NR2A) {2.1.3.2} (TFClass)
TFClass ID	TFClass: 2.1.3.2.1
HGNC	HGNC:5024
MGI	MGI:109128
EntrezGene (human)	GeneID:3172 (SSTAR profile)
EntrezGene (mouse)	GeneID:15378 (SSTAR profile)
UniProt ID (human)	HNF4A_HUMAN
UniProt ID (mouse)	HNF4A_MOUSE
UniProt AC (human)	P41235 (TFClass)
UniProt AC (mouse)	P49698 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	26 human, 25 mouse
HT-SELEX	6
Methyl-HT-SELEX	1

PCM	HNF4A.H12INVIVO.0.PSM.A.pcm
PWM	HNF4A.H12INVIVO.0.PSM.A.pwm
PFM	HNF4A.H12INVIVO.0.PSM.A.pfm
Alignment	HNF4A.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	HNF4A.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	HNF4A.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	HNF4A.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	HNF4A.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	HNF4A.H12INVIVO.0.PSM.A_homer_format_0.001.txt HNF4A.H12INVIVO.0.PSM.A_homer_format_0.0005.txt HNF4A.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	285.0	205.0	389.0	121.0
02	446.0	37.0	430.0	87.0
03	77.0	41.0	818.0	64.0
04	152.0	44.0	392.0	412.0
05	133.0	342.0	263.0	262.0
06	6.0	920.0	7.0	67.0
07	960.0	5.0	34.0	1.0
08	929.0	7.0	53.0	11.0
09	920.0	1.0	74.0	5.0
10	4.0	5.0	982.0	9.0
11	6.0	5.0	177.0	812.0
12	48.0	658.0	66.0	228.0
13	5.0	892.0	9.0	94.0
14	711.0	70.0	106.0	113.0

PFM

	A	C	G	T
01	0.285	0.205	0.389	0.121
02	0.446	0.037	0.43	0.087
03	0.077	0.041	0.818	0.064
04	0.152	0.044	0.392	0.412
05	0.133	0.342	0.263	0.262
06	0.006	0.92	0.007	0.067
07	0.96	0.005	0.034	0.001
08	0.929	0.007	0.053	0.011
09	0.92	0.001	0.074	0.005
10	0.004	0.005	0.982	0.009
11	0.006	0.005	0.177	0.812
12	0.048	0.658	0.066	0.228
13	0.005	0.892	0.009	0.094
14	0.711	0.07	0.106	0.113

PWM

	A	C	G	T
01	0.13	-0.197	0.44	-0.718
02	0.576	-1.872	0.539	-1.043
03	-1.162	-1.774	1.181	-1.343
04	-0.493	-1.706	0.447	0.497
05	-0.625	0.312	0.05	0.047
06	-3.484	1.298	-3.362	-1.298
07	1.34	-3.622	-1.952	-4.525
08	1.308	-3.362	-1.526	-2.985
09	1.298	-4.525	-1.201	-3.622
10	-3.783	-3.622	1.363	-3.156
11	-3.484	-3.622	-0.342	1.173
12	-1.622	0.963	-1.313	-0.091
13	-3.622	1.267	-3.156	-0.967
14	1.041	-1.255	-0.849	-0.786

Standard thresholds

P-value	Threshold
0.001	3.26526
0.0005	4.38826
0.0001	6.75756