COT1.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	COT1.H12RSNP.0.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	0
Quality	A

Motif length	14
Consensus	nhRAGGTCAWRRSb
GC content	49.03%
Information content (bits; total / per base)	14.309 / 1.022
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1610

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)	0.861	0.901	0.74	0.808	0.846	0.9	2.774	3.321	150.619	287.215

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.996	0.993	0.986	0.98	0.928	0.926
Overall, 8 experiments	best	1.0	1.0	0.999	0.998	0.991	0.987
Methyl HT-SELEX, 2 experiments	median	0.998	0.997	0.994	0.991	0.98	0.974
Methyl HT-SELEX, 2 experiments	best	1.0	0.999	0.997	0.996	0.981	0.974
Non-Methyl HT-SELEX, 6 experiments	median	0.995	0.992	0.972	0.965	0.862	0.86
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	0.999	0.998	0.991	0.987

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.149	8.176	0.159	0.093

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.0.PSM.A.pcm
PWM	COT1.H12RSNP.0.PSM.A.pwm
PFM	COT1.H12RSNP.0.PSM.A.pfm
Alignment	COT1.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	COT1.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	COT1.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	COT1.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	COT1.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	COT1.H12RSNP.0.PSM.A_homer_format_0.001.txt COT1.H12RSNP.0.PSM.A_homer_format_0.0005.txt COT1.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	362.75	495.75	350.75	400.75
02	807.0	227.0	222.0	354.0
03	872.0	99.0	543.0	96.0
04	1321.0	3.0	286.0	0.0
05	0.0	0.0	1610.0	0.0
06	0.0	0.0	1610.0	0.0
07	0.0	0.0	0.0	1610.0
08	0.0	1606.0	0.0	4.0
09	1609.0	0.0	1.0	0.0
10	975.0	161.0	69.0	405.0
11	900.0	105.0	485.0	120.0
12	441.0	92.0	934.0	143.0
13	156.0	191.0	1127.0	136.0
14	182.25	271.25	563.25	593.25

PFM

	A	C	G	T
01	0.225	0.308	0.218	0.249
02	0.501	0.141	0.138	0.22
03	0.542	0.061	0.337	0.06
04	0.82	0.002	0.178	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.998	0.0	0.002
09	0.999	0.0	0.001	0.0
10	0.606	0.1	0.043	0.252
11	0.559	0.065	0.301	0.075
12	0.274	0.057	0.58	0.089
13	0.097	0.119	0.7	0.084
14	0.113	0.168	0.35	0.368

PWM

	A	C	G	T
01	-0.103	0.208	-0.137	-0.004
02	0.693	-0.569	-0.591	-0.128
03	0.771	-1.389	0.298	-1.419
04	1.185	-4.424	-0.34	-5.389
05	-5.389	-5.389	1.383	-5.389
06	-5.389	-5.389	1.383	-5.389
07	-5.389	-5.389	-5.389	1.383
08	-5.389	1.38	-5.389	-4.237
09	1.382	-5.389	-4.956	-5.389
10	0.882	-0.909	-1.742	0.006
11	0.802	-1.331	0.186	-1.2
12	0.091	-1.461	0.839	-1.027
13	-0.941	-0.74	1.027	-1.076
14	-0.787	-0.392	0.335	0.386

Standard thresholds

P-value	Threshold
0.001	1.93456
0.0005	3.41681
0.0001	6.93981