HNF4A.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HNF4A.H12RSNP.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	15
Consensus	vRGKbCAAAGTYCvn
GC content	51.44%
Information content (bits; total / per base)	13.677 / 0.912
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8591

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)	0.956	0.988	0.917	0.97	0.931	0.977	4.262	5.242	356.444	623.824
Mouse	25 (165)	0.942	0.971	0.882	0.94	0.913	0.956	3.539	4.375	321.745	472.18

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.861	0.869	0.674	0.701	0.581	0.614
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	0.916	0.926	0.716	0.761
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.916	0.926	0.716	0.761
Non-Methyl HT-SELEX, 6 experiments	median	0.776	0.794	0.62	0.652	0.554	0.584
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
#	19.595	40.162	0.427	0.36

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.H12RSNP.0.PSM.A.pcm
PWM	HNF4A.H12RSNP.0.PSM.A.pwm
PFM	HNF4A.H12RSNP.0.PSM.A.pfm
Alignment	HNF4A.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	HNF4A.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	HNF4A.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	HNF4A.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	HNF4A.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	HNF4A.H12RSNP.0.PSM.A_homer_format_0.001.txt HNF4A.H12RSNP.0.PSM.A_homer_format_0.0005.txt HNF4A.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1999.0	1531.0	3889.0	1172.0
02	2743.0	541.0	4817.0	490.0
03	417.0	290.0	7370.0	514.0
04	843.0	406.0	3239.0	4103.0
05	970.0	3038.0	1450.0	3133.0
06	167.0	7535.0	265.0	624.0
07	7722.0	81.0	709.0	79.0
08	8167.0	58.0	205.0	161.0
09	8279.0	33.0	226.0	53.0
10	28.0	27.0	8486.0	50.0
11	146.0	102.0	1472.0	6871.0
12	685.0	4833.0	556.0	2517.0
13	174.0	7485.0	235.0	697.0
14	4676.25	976.25	2084.25	854.25
15	2242.75	2708.75	1644.75	1994.75

PFM

	A	C	G	T
01	0.233	0.178	0.453	0.136
02	0.319	0.063	0.561	0.057
03	0.049	0.034	0.858	0.06
04	0.098	0.047	0.377	0.478
05	0.113	0.354	0.169	0.365
06	0.019	0.877	0.031	0.073
07	0.899	0.009	0.083	0.009
08	0.951	0.007	0.024	0.019
09	0.964	0.004	0.026	0.006
10	0.003	0.003	0.988	0.006
11	0.017	0.012	0.171	0.8
12	0.08	0.563	0.065	0.293
13	0.02	0.871	0.027	0.081
14	0.544	0.114	0.243	0.099
15	0.261	0.315	0.191	0.232

PWM

	A	C	G	T
01	-0.072	-0.338	0.593	-0.605
02	0.244	-1.376	0.807	-1.474
03	-1.635	-1.996	1.232	-1.427
04	-0.934	-1.661	0.41	0.647
05	-0.794	0.346	-0.392	0.377
06	-2.542	1.254	-2.085	-1.233
07	1.279	-3.251	-1.106	-3.276
08	1.335	-3.574	-2.339	-2.578
09	1.349	-4.11	-2.243	-3.661
10	-4.263	-4.297	1.373	-3.717
11	-2.674	-3.026	-0.377	1.162
12	-1.141	0.81	-1.348	0.158
13	-2.501	1.248	-2.204	-1.123
14	0.778	-0.787	-0.03	-0.92
15	0.043	0.232	-0.267	-0.074

Standard thresholds

P-value	Threshold
0.001	3.46476
0.0005	4.56316
0.0001	6.84751