COT1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	COT1.H12INVIVO.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	12
Consensus	bhRAGGTCAvvv
GC content	56.19%
Information content (bits; total / per base)	10.776 / 0.898
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000

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)	0.866	0.91	0.738	0.808	0.867	0.902	3.042	3.386	174.988	317.796

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.991	0.984	0.981	0.971	0.922	0.917
Overall, 8 experiments	best	0.999	0.998	0.997	0.995	0.991	0.987
Methyl HT-SELEX, 2 experiments	median	0.996	0.994	0.993	0.989	0.98	0.973
Methyl HT-SELEX, 2 experiments	best	0.998	0.996	0.995	0.992	0.981	0.974
Non-Methyl HT-SELEX, 6 experiments	median	0.985	0.975	0.958	0.944	0.847	0.842
Non-Methyl HT-SELEX, 6 experiments	best	0.999	0.998	0.997	0.995	0.991	0.987

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.248	4.735	0.155	0.096

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.H12INVIVO.0.PSM.A.pcm
PWM	COT1.H12INVIVO.0.PSM.A.pwm
PFM	COT1.H12INVIVO.0.PSM.A.pfm
Alignment	COT1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	COT1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	COT1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	COT1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	COT1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	COT1.H12INVIVO.0.PSM.A_homer_format_0.001.txt COT1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt COT1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	155.0	498.0	190.0	157.0
02	535.0	194.0	115.0	156.0
03	420.0	71.0	467.0	42.0
04	726.0	1.0	265.0	8.0
05	8.0	4.0	983.0	5.0
06	6.0	3.0	980.0	11.0
07	7.0	50.0	52.0	891.0
08	2.0	931.0	51.0	16.0
09	931.0	10.0	51.0	8.0
10	281.0	267.0	367.0	85.0
11	335.0	147.0	393.0	125.0
12	226.0	163.0	490.0	121.0

PFM

	A	C	G	T
01	0.155	0.498	0.19	0.157
02	0.535	0.194	0.115	0.156
03	0.42	0.071	0.467	0.042
04	0.726	0.001	0.265	0.008
05	0.008	0.004	0.983	0.005
06	0.006	0.003	0.98	0.011
07	0.007	0.05	0.052	0.891
08	0.002	0.931	0.051	0.016
09	0.931	0.01	0.051	0.008
10	0.281	0.267	0.367	0.085
11	0.335	0.147	0.393	0.125
12	0.226	0.163	0.49	0.121

PWM

	A	C	G	T
01	-0.474	0.686	-0.272	-0.461
02	0.757	-0.252	-0.769	-0.467
03	0.516	-1.242	0.622	-1.75
04	1.062	-4.525	0.058	-3.253
05	-3.253	-3.783	1.364	-3.622
06	-3.484	-3.975	1.361	-2.985
07	-3.362	-1.582	-1.544	1.266
08	-4.213	1.31	-1.563	-2.653
09	1.31	-3.066	-1.563	-3.253
10	0.116	0.065	0.382	-1.066
11	0.291	-0.526	0.45	-0.686
12	-0.1	-0.424	0.67	-0.718

Standard thresholds

P-value	Threshold
0.001	4.50441
0.0005	5.46257
0.0001	7.492255