COT1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	COT1.H12INVITRO.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	10
Consensus	ndRGGTCAnn
GC content	52.95%
Information content (bits; total / per base)	9.29 / 0.929
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9822

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)	0.873	0.915	0.763	0.84	0.837	0.893	2.624	3.115	177.361	321.102

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.997	0.995	0.987	0.983	0.959	0.95
Overall, 8 experiments	best	1.0	1.0	0.998	0.998	0.991	0.988
Methyl HT-SELEX, 2 experiments	median	0.997	0.996	0.993	0.99	0.98	0.974
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.995	0.993	0.982	0.974
Non-Methyl HT-SELEX, 6 experiments	median	0.997	0.995	0.976	0.971	0.934	0.915
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	0.998	0.998	0.991	0.988

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.506	5.744	0.185	0.103

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.H12INVITRO.0.PSM.A.pcm
PWM	COT1.H12INVITRO.0.PSM.A.pwm
PFM	COT1.H12INVITRO.0.PSM.A.pfm
Alignment	COT1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	COT1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	COT1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	COT1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	COT1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	COT1.H12INVITRO.0.PSM.A_homer_format_0.001.txt COT1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt COT1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3255.5	1973.5	2112.5	2480.5
02	3663.0	1028.0	3731.0	1400.0
03	5771.0	316.0	3264.0	471.0
04	5.0	89.0	9618.0	110.0
05	0.0	14.0	9776.0	32.0
06	17.0	10.0	87.0	9708.0
07	158.0	8995.0	371.0	298.0
08	8306.0	324.0	956.0	236.0
09	3365.75	2386.75	1828.75	2240.75
10	2976.25	1777.25	3351.25	1717.25

PFM

	A	C	G	T
01	0.331	0.201	0.215	0.253
02	0.373	0.105	0.38	0.143
03	0.588	0.032	0.332	0.048
04	0.001	0.009	0.979	0.011
05	0.0	0.001	0.995	0.003
06	0.002	0.001	0.009	0.988
07	0.016	0.916	0.038	0.03
08	0.846	0.033	0.097	0.024
09	0.343	0.243	0.186	0.228
10	0.303	0.181	0.341	0.175

PWM

	A	C	G	T
01	0.282	-0.218	-0.15	0.01
02	0.4	-0.869	0.418	-0.561
03	0.854	-2.044	0.284	-1.647
04	-5.819	-3.293	1.365	-3.086
05	-6.975	-5.016	1.381	-4.272
06	-4.847	-5.298	-3.315	1.374
07	-2.73	1.298	-1.885	-2.102
08	1.218	-2.019	-0.942	-2.333
09	0.315	-0.028	-0.294	-0.091
10	0.192	-0.323	0.311	-0.357

Standard thresholds

P-value	Threshold
0.001	4.8738
0.0005	5.871465
0.0001	7.67062