HNF4A.H14INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HNF4A.H14INVITRO.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	vdGdbCAAAGKYCR
GC content	54.16%
Information content (bits; total / per base)	13.038 / 0.931
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1002
Previous names	HNF4A.H12INVITRO.0.PSM.A

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)	0.957	0.987	0.917	0.969	0.937	0.978	4.266	5.131	358.886	615.409
Mouse	25 (165)	0.942	0.969	0.874	0.934	0.92	0.952	3.635	4.283	321.638	460.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.888	0.892	0.695	0.719	0.595	0.627
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	0.924	0.931	0.738	0.774
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.924	0.931	0.738	0.774
Non-Methyl HT-SELEX, 6 experiments	median	0.794	0.808	0.638	0.665	0.566	0.593
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
#	9.687	27.779	0.413	0.345

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	HNF4A.H14INVITRO.0.PSM.A.pcm
PWM	HNF4A.H14INVITRO.0.PSM.A.pwm
PFM	HNF4A.H14INVITRO.0.PSM.A.pfm
Threshold to P-value map	HNF4A.H14INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	HNF4A.H14INVITRO.0.PSM.A_jaspar_format.txt
MEME format	HNF4A.H14INVITRO.0.PSM.A_meme_format.meme
Transfac format	HNF4A.H14INVITRO.0.PSM.A_transfac_format.txt
Homer format	HNF4A.H14INVITRO.0.PSM.A_homer_format_0.001.txt HNF4A.H14INVITRO.0.PSM.A_homer_format_0.0005.txt HNF4A.H14INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	246.0	211.0	441.0	104.0
02	357.0	63.0	488.0	94.0
03	85.0	29.0	844.0	44.0
04	137.0	58.0	483.0	324.0
05	88.0	351.0	311.0	252.0
06	18.0	904.0	24.0	56.0
07	915.0	10.0	72.0	5.0
08	881.0	13.0	97.0	11.0
09	886.0	2.0	104.0	10.0
10	7.0	4.0	967.0	24.0
11	19.0	8.0	324.0	651.0
12	29.0	575.0	102.0	296.0
13	19.0	885.0	17.0	81.0
14	696.0	60.0	150.0	96.0

PFM

	A	C	G	T
01	0.246	0.211	0.44	0.104
02	0.356	0.063	0.487	0.094
03	0.085	0.029	0.842	0.044
04	0.137	0.058	0.482	0.323
05	0.088	0.35	0.31	0.251
06	0.018	0.902	0.024	0.056
07	0.913	0.01	0.072	0.005
08	0.879	0.013	0.097	0.011
09	0.884	0.002	0.104	0.01
10	0.007	0.004	0.965	0.024
11	0.019	0.008	0.323	0.65
12	0.029	0.574	0.102	0.295
13	0.019	0.883	0.017	0.081
14	0.695	0.06	0.15	0.096

PWM

	A	C	G	T
01	-0.018	-0.17	0.563	-0.869
02	0.352	-1.36	0.664	-0.969
03	-1.068	-2.105	1.21	-1.708
04	-0.598	-1.441	0.653	0.256
05	-1.034	0.335	0.215	0.006
06	-2.548	1.278	-2.283	-1.475
07	1.29	-3.068	-1.23	-3.624
08	1.253	-2.841	-0.938	-2.987
09	1.258	-4.215	-0.869	-3.068
10	-3.364	-3.785	1.346	-2.283
11	-2.499	-3.255	0.256	0.951
12	-2.105	0.827	-0.889	0.166
13	-2.499	1.257	-2.6	-1.115
14	1.017	-1.408	-0.508	-0.948

Standard thresholds

P-value	Threshold
0.001	3.84286
0.0005	4.86616
0.0001	6.99386