NR1D2.H12RSNP.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR1D2.H12RSNP.1.SM.D
Gene (human)	NR1D2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nr1d2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	17
Consensus	nbAGGTCAGTRGGTCRn
GC content	54.93%
Information content (bits; total / per base)	20.541 / 1.208
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9974

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
Mouse	2 (12)	0.691	0.776	0.581	0.693	0.668	0.754	2.299	2.873	76.615	141.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	1.0	1.0	0.966	0.968	0.798	0.821
Overall, 2 experiments	best	1.0	1.0	0.975	0.975	0.814	0.834
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.958	0.961	0.782	0.809
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.958	0.961	0.782	0.809
Non-Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.975	0.975	0.814	0.834
Non-Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.975	0.975	0.814	0.834

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	Thyroid hormone receptor-related {2.1.2} (TFClass)
TF subfamily	REVERBA (NR1D) {2.1.2.3} (TFClass)
TFClass ID	TFClass: 2.1.2.3.2
HGNC	HGNC:7963
MGI	MGI:2449205
EntrezGene (human)	GeneID:9975 (SSTAR profile)
EntrezGene (mouse)	GeneID:353187 (SSTAR profile)
UniProt ID (human)	NR1D2_HUMAN
UniProt ID (mouse)	NR1D2_MOUSE
UniProt AC (human)	Q14995 (TFClass)
UniProt AC (mouse)	Q60674 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	NR1D2.H12RSNP.1.SM.D.pcm
PWM	NR1D2.H12RSNP.1.SM.D.pwm
PFM	NR1D2.H12RSNP.1.SM.D.pfm
Alignment	NR1D2.H12RSNP.1.SM.D.words.tsv
Threshold to P-value map	NR1D2.H12RSNP.1.SM.D.thr
Motif in other formats
JASPAR format	NR1D2.H12RSNP.1.SM.D_jaspar_format.txt
MEME format	NR1D2.H12RSNP.1.SM.D_meme_format.meme
Transfac format	NR1D2.H12RSNP.1.SM.D_transfac_format.txt
Homer format	NR1D2.H12RSNP.1.SM.D_homer_format_0.001.txt NR1D2.H12RSNP.1.SM.D_homer_format_0.0005.txt NR1D2.H12RSNP.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1901.5	2018.5	3843.5	2210.5
02	1234.5	1503.5	1921.5	5314.5
03	7054.0	69.0	2801.0	50.0
04	41.0	41.0	9682.0	210.0
05	35.0	21.0	9882.0	36.0
06	42.0	69.0	536.0	9327.0
07	93.0	7157.0	50.0	2674.0
08	9852.0	6.0	93.0	23.0
09	315.0	767.0	8676.0	216.0
10	32.0	170.0	189.0	9583.0
11	5372.0	21.0	4559.0	22.0
12	40.0	14.0	9556.0	364.0
13	87.0	45.0	9794.0	48.0
14	239.0	341.0	980.0	8414.0
15	59.0	9245.0	179.0	491.0
16	6371.5	376.5	2820.5	405.5
17	2269.75	2546.75	3156.75	2000.75

PFM

	A	C	G	T
01	0.191	0.202	0.385	0.222
02	0.124	0.151	0.193	0.533
03	0.707	0.007	0.281	0.005
04	0.004	0.004	0.971	0.021
05	0.004	0.002	0.991	0.004
06	0.004	0.007	0.054	0.935
07	0.009	0.718	0.005	0.268
08	0.988	0.001	0.009	0.002
09	0.032	0.077	0.87	0.022
10	0.003	0.017	0.019	0.961
11	0.539	0.002	0.457	0.002
12	0.004	0.001	0.958	0.036
13	0.009	0.005	0.982	0.005
14	0.024	0.034	0.098	0.844
15	0.006	0.927	0.018	0.049
16	0.639	0.038	0.283	0.041
17	0.228	0.255	0.316	0.201

PWM

	A	C	G	T
01	-0.271	-0.211	0.432	-0.12
02	-0.702	-0.505	-0.26	0.756
03	1.039	-3.555	0.116	-3.865
04	-4.054	-4.054	1.356	-2.464
05	-4.203	-4.674	1.376	-4.177
06	-4.031	-3.555	-1.534	1.319
07	-3.265	1.054	-3.865	0.07
08	1.373	-5.706	-3.265	-4.591
09	-2.063	-1.177	1.246	-2.436
10	-4.287	-2.673	-2.569	1.346
11	0.767	-4.674	0.603	-4.632
12	-4.078	-5.031	1.343	-1.919
13	-3.33	-3.966	1.367	-3.904
14	-2.336	-1.984	-0.932	1.216
15	-3.707	1.31	-2.622	-1.621
16	0.938	-1.885	0.123	-1.812
17	-0.094	0.021	0.236	-0.22

Standard thresholds

P-value	Threshold
0.001	-1.20284
0.0005	0.40641
0.0001	3.80981