NR5A2.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR5A2.H12INVITRO.0.PSM.A
Gene (human)	NR5A2 (GeneCards)
Gene synonyms (human)	B1F, CPF, FTF
Gene (mouse)	Nr5a2
Gene synonyms (mouse)	Lrh1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	nYCAAGGTCRn
GC content	53.08%
Information content (bits; total / per base)	13.055 / 1.187
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9041

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	1 (5)	0.875	0.9	0.79	0.818	0.842	0.864	2.92	2.996	145.854	182.347
Mouse	6 (34)	0.902	0.932	0.808	0.882	0.883	0.928	3.318	3.671	131.181	381.071

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.985	0.982	0.793	0.813	0.652	0.688
Overall, 2 experiments	best	0.991	0.988	0.814	0.832	0.654	0.696
Methyl HT-SELEX, 1 experiments	median	0.98	0.977	0.772	0.794	0.65	0.68
Methyl HT-SELEX, 1 experiments	best	0.98	0.977	0.772	0.794	0.65	0.68
Non-Methyl HT-SELEX, 1 experiments	median	0.991	0.988	0.814	0.832	0.654	0.696
Non-Methyl HT-SELEX, 1 experiments	best	0.991	0.988	0.814	0.832	0.654	0.696

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	FTZF1-related (NR5A) {2.1.5} (TFClass)
TF subfamily	{2.1.5.0} (TFClass)
TFClass ID	TFClass: 2.1.5.0.2
HGNC	HGNC:7984
MGI	MGI:1346834
EntrezGene (human)	GeneID:2494 (SSTAR profile)
EntrezGene (mouse)	GeneID:26424 (SSTAR profile)
UniProt ID (human)	NR5A2_HUMAN
UniProt ID (mouse)	NR5A2_MOUSE
UniProt AC (human)	O00482 (TFClass)
UniProt AC (mouse)	P45448 (TFClass)
GRECO-DB-TF	yes

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

PCM	NR5A2.H12INVITRO.0.PSM.A.pcm
PWM	NR5A2.H12INVITRO.0.PSM.A.pwm
PFM	NR5A2.H12INVITRO.0.PSM.A.pfm
Alignment	NR5A2.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	NR5A2.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	NR5A2.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	NR5A2.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	NR5A2.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	NR5A2.H12INVITRO.0.PSM.A_homer_format_0.001.txt NR5A2.H12INVITRO.0.PSM.A_homer_format_0.0005.txt NR5A2.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1510.5	2128.5	2956.5	2445.5
02	408.5	1676.5	949.5	6006.5
03	50.0	7146.0	1736.0	109.0
04	8692.0	2.0	335.0	12.0
05	9037.0	0.0	1.0	3.0
06	0.0	0.0	9041.0	0.0
07	0.0	1.0	9039.0	1.0
08	243.0	931.0	182.0	7685.0
09	102.0	8241.0	424.0	274.0
10	5391.75	212.75	3245.75	190.75
11	1751.25	3083.25	1455.25	2751.25

PFM

	A	C	G	T
01	0.167	0.235	0.327	0.27
02	0.045	0.185	0.105	0.664
03	0.006	0.79	0.192	0.012
04	0.961	0.0	0.037	0.001
05	1.0	0.0	0.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	1.0	0.0
08	0.027	0.103	0.02	0.85
09	0.011	0.912	0.047	0.03
10	0.596	0.024	0.359	0.021
11	0.194	0.341	0.161	0.304

PWM

	A	C	G	T
01	-0.403	-0.06	0.268	0.079
02	-1.706	-0.298	-0.866	0.977
03	-3.768	1.15	-0.264	-3.012
04	1.346	-6.271	-1.903	-5.066
05	1.385	-6.901	-6.537	-6.061
06	-6.901	-6.901	1.386	-6.901
07	-6.901	-6.537	1.385	-6.537
08	-2.222	-0.886	-2.508	1.223
09	-3.077	1.293	-1.669	-2.103
10	0.869	-2.353	0.362	-2.461
11	-0.255	0.31	-0.44	0.196

Standard thresholds

P-value	Threshold
0.001	3.052315
0.0005	4.51408
0.0001	7.1762