COT1.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	COT1.H12RSNP.1.PSM.A
Gene (human)	NR2F1 (GeneCards)
Gene synonyms (human)	EAR3, ERBAL3, TFCOUP1
Gene (mouse)	Nr2f1
Gene synonyms (mouse)	Erbal3, Tfcoup1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	16
Consensus	dRGKYCAAAGGTCAnn
GC content	49.79%
Information content (bits; total / per base)	18.652 / 1.166
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1551

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	5 (34)	0.858	0.895	0.767	0.836	0.821	0.86	2.929	3.683	139.58	214.215

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.999	0.998	0.974	0.971	0.93	0.92
Overall, 8 experiments	best	1.0	1.0	1.0	1.0	0.989	0.987
Methyl HT-SELEX, 2 experiments	median	1.0	1.0	0.998	0.997	0.977	0.974
Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.999	0.979	0.975
Non-Methyl HT-SELEX, 6 experiments	median	0.995	0.994	0.952	0.944	0.886	0.861
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	1.0	1.0	0.989	0.987

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.769	6.801	0.152	0.097

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	COUP (NR2F) {2.1.3.5} (TFClass)
TFClass ID	TFClass: 2.1.3.5.1
HGNC	HGNC:7975
MGI	MGI:1352451
EntrezGene (human)	GeneID:7025 (SSTAR profile)
EntrezGene (mouse)	GeneID:13865 (SSTAR profile)
UniProt ID (human)	COT1_HUMAN
UniProt ID (mouse)	COT1_MOUSE
UniProt AC (human)	P10589 (TFClass)
UniProt AC (mouse)	Q60632 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	COT1.H12RSNP.1.PSM.A.pcm
PWM	COT1.H12RSNP.1.PSM.A.pwm
PFM	COT1.H12RSNP.1.PSM.A.pfm
Alignment	COT1.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	COT1.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	COT1.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	COT1.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	COT1.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	COT1.H12RSNP.1.PSM.A_homer_format_0.001.txt COT1.H12RSNP.1.PSM.A_homer_format_0.0005.txt COT1.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	532.0	190.0	614.0	215.0
02	612.25	63.25	812.25	63.25
03	45.0	59.0	1359.0	88.0
04	44.0	73.0	1109.0	325.0
05	49.0	343.0	50.0	1109.0
06	310.0	1175.0	25.0	41.0
07	1450.0	35.0	18.0	48.0
08	1318.0	12.0	144.0	77.0
09	1477.0	0.0	73.0	1.0
10	0.0	0.0	1549.0	2.0
11	0.0	0.0	1551.0	0.0
12	0.0	1.0	4.0	1546.0
13	0.0	1501.0	17.0	33.0
14	1437.0	7.0	100.0	7.0
15	571.75	369.75	212.75	396.75
16	387.75	310.75	578.75	273.75

PFM

	A	C	G	T
01	0.343	0.123	0.396	0.139
02	0.395	0.041	0.524	0.041
03	0.029	0.038	0.876	0.057
04	0.028	0.047	0.715	0.21
05	0.032	0.221	0.032	0.715
06	0.2	0.758	0.016	0.026
07	0.935	0.023	0.012	0.031
08	0.85	0.008	0.093	0.05
09	0.952	0.0	0.047	0.001
10	0.0	0.0	0.999	0.001
11	0.0	0.0	1.0	0.0
12	0.0	0.001	0.003	0.997
13	0.0	0.968	0.011	0.021
14	0.926	0.005	0.064	0.005
15	0.369	0.238	0.137	0.256
16	0.25	0.2	0.373	0.176

PWM

	A	C	G	T
01	0.315	-0.708	0.458	-0.586
02	0.455	-1.789	0.737	-1.789
03	-2.118	-1.857	1.251	-1.467
04	-2.14	-1.65	1.048	-0.176
05	-2.036	-0.122	-2.017	1.048
06	-0.223	1.105	-2.675	-2.208
07	1.315	-2.359	-2.978	-2.056
08	1.22	-3.338	-0.983	-1.598
09	1.334	-5.357	-1.65	-4.922
10	-5.357	-5.357	1.381	-4.62
11	-5.357	-5.357	1.383	-5.357
12	-5.357	-4.922	-4.201	1.38
13	-5.357	1.35	-3.029	-2.414
14	1.307	-3.786	-1.342	-3.786
15	0.387	-0.047	-0.596	0.023
16	0.0	-0.22	0.399	-0.346

Standard thresholds

P-value	Threshold
0.001	0.22731
0.0005	1.76991
0.0001	4.97871