COT1.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	COT1.H12INVIVO.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	17
Consensus	vvvdbvhRAGGTCAvvd
GC content	57.76%
Information content (bits; total / per base)	11.78 / 0.693
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)	0.85	0.9	0.744	0.813	0.849	0.885	3.296	3.584	143.535	249.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.988	0.981	0.965	0.954	0.888	0.885
Overall, 8 experiments	best	1.0	1.0	0.998	0.998	0.986	0.982
Methyl HT-SELEX, 2 experiments	median	0.998	0.997	0.992	0.99	0.971	0.964
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.995	0.994	0.972	0.965
Non-Methyl HT-SELEX, 6 experiments	median	0.978	0.967	0.933	0.916	0.797	0.8
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	0.998	0.998	0.986	0.982

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.074	3.926	0.105	0.081

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.1.PSM.A.pcm
PWM	COT1.H12INVIVO.1.PSM.A.pwm
PFM	COT1.H12INVIVO.1.PSM.A.pfm
Alignment	COT1.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	COT1.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	COT1.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	COT1.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	COT1.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	COT1.H12INVIVO.1.PSM.A_homer_format_0.001.txt COT1.H12INVIVO.1.PSM.A_homer_format_0.0005.txt COT1.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	239.0	192.0	430.0	139.0
02	343.0	130.0	416.0	111.0
03	246.0	142.0	488.0	124.0
04	206.0	126.0	517.0	151.0
05	108.0	228.0	343.0	321.0
06	144.0	516.0	200.0	140.0
07	643.0	120.0	117.0	120.0
08	417.0	53.0	506.0	24.0
09	695.0	1.0	304.0	0.0
10	15.0	0.0	970.0	15.0
11	15.0	2.0	973.0	10.0
12	6.0	65.0	152.0	777.0
13	9.0	921.0	33.0	37.0
14	967.0	4.0	17.0	12.0
15	243.0	190.0	477.0	90.0
16	354.0	181.0	351.0	114.0
17	194.0	146.0	509.0	151.0

PFM

	A	C	G	T
01	0.239	0.192	0.43	0.139
02	0.343	0.13	0.416	0.111
03	0.246	0.142	0.488	0.124
04	0.206	0.126	0.517	0.151
05	0.108	0.228	0.343	0.321
06	0.144	0.516	0.2	0.14
07	0.643	0.12	0.117	0.12
08	0.417	0.053	0.506	0.024
09	0.695	0.001	0.304	0.0
10	0.015	0.0	0.97	0.015
11	0.015	0.002	0.973	0.01
12	0.006	0.065	0.152	0.777
13	0.009	0.921	0.033	0.037
14	0.967	0.004	0.017	0.012
15	0.243	0.19	0.477	0.09
16	0.354	0.181	0.351	0.114
17	0.194	0.146	0.509	0.151

PWM

	A	C	G	T
01	-0.045	-0.262	0.539	-0.582
02	0.314	-0.648	0.506	-0.803
03	-0.016	-0.56	0.666	-0.694
04	-0.192	-0.678	0.723	-0.5
05	-0.83	-0.091	0.314	0.248
06	-0.547	0.721	-0.221	-0.574
07	0.94	-0.727	-0.752	-0.727
08	0.509	-1.526	0.702	-2.281
09	1.018	-4.525	0.194	-4.982
10	-2.711	-4.982	1.351	-2.711
11	-2.711	-4.213	1.354	-3.066
12	-3.484	-1.328	-0.493	1.129
13	-3.156	1.299	-1.981	-1.872
14	1.348	-3.783	-2.598	-2.909
15	-0.028	-0.272	0.643	-1.01
16	0.346	-0.32	0.337	-0.777
17	-0.252	-0.533	0.707	-0.5

Standard thresholds

P-value	Threshold
0.001	4.24141
0.0005	5.24291
0.0001	7.27606