NR2C2.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NR2C2.H12INVITRO.0.SM.B
Gene (human)	NR2C2 (GeneCards)
Gene synonyms (human)	TAK1, TR4
Gene (mouse)	Nr2c2
Gene synonyms (mouse)	Mtr2r1, Tak1, Tr4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	9
Consensus	ndAGGTCAn
GC content	48.48%
Information content (bits; total / per base)	9.847 / 1.094
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8928

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	4 (27)	0.653	0.8	0.542	0.708	0.629	0.8	1.692	2.578	44.959	97.097

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.951	0.931	0.908	0.876	0.76	0.765
Overall, 4 experiments	best	0.994	0.993	0.951	0.936	0.91	0.88
Methyl HT-SELEX, 1 experiments	median	0.967	0.945	0.951	0.923	0.91	0.88
Methyl HT-SELEX, 1 experiments	best	0.967	0.945	0.951	0.923	0.91	0.88
Non-Methyl HT-SELEX, 3 experiments	median	0.935	0.917	0.876	0.83	0.759	0.742
Non-Methyl HT-SELEX, 3 experiments	best	0.994	0.993	0.94	0.936	0.761	0.787

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	TR (NR2C) {2.1.3.4} (TFClass)
TFClass ID	TFClass: 2.1.3.4.2
HGNC	HGNC:7972
MGI	MGI:1352466
EntrezGene (human)	GeneID:7182 (SSTAR profile)
EntrezGene (mouse)	GeneID:22026 (SSTAR profile)
UniProt ID (human)	NR2C2_HUMAN
UniProt ID (mouse)	NR2C2_MOUSE
UniProt AC (human)	P49116 (TFClass)
UniProt AC (mouse)	P49117 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	4 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	NR2C2.H12INVITRO.0.SM.B.pcm
PWM	NR2C2.H12INVITRO.0.SM.B.pwm
PFM	NR2C2.H12INVITRO.0.SM.B.pfm
Alignment	NR2C2.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	NR2C2.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	NR2C2.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	NR2C2.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	NR2C2.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	NR2C2.H12INVITRO.0.SM.B_homer_format_0.001.txt NR2C2.H12INVITRO.0.SM.B_homer_format_0.0005.txt NR2C2.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3253.5	1744.5	1730.5	2199.5
02	4557.25	800.25	2470.25	1100.25
03	6740.0	60.0	2110.0	18.0
04	0.0	0.0	8928.0	0.0
05	0.0	0.0	8928.0	0.0
06	0.0	0.0	0.0	8928.0
07	53.25	6994.25	185.25	1695.25
08	7403.5	166.5	1263.5	94.5
09	2691.5	2172.5	1402.5	2661.5

PFM

	A	C	G	T
01	0.364	0.195	0.194	0.246
02	0.51	0.09	0.277	0.123
03	0.755	0.007	0.236	0.002
04	0.0	0.0	1.0	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.0	1.0
07	0.006	0.783	0.021	0.19
08	0.829	0.019	0.142	0.011
09	0.301	0.243	0.157	0.298

PWM

	A	C	G	T
01	0.377	-0.246	-0.254	-0.015
02	0.713	-1.024	0.101	-0.706
03	1.104	-3.58	-0.056	-4.702
04	-6.89	-6.89	1.386	-6.89
05	-6.89	-6.89	1.386	-6.89
06	-6.89	-6.89	-6.89	1.386
07	-3.695	1.141	-2.478	-0.275
08	1.198	-2.583	-0.568	-3.139
09	0.187	-0.027	-0.464	0.176

Standard thresholds

P-value	Threshold
0.001	5.08434
0.0005	6.20822
0.0001	7.610845