GCR.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GCR.H12INVIVO.0.PS.A
Gene (human)	NR3C1 (GeneCards)
Gene synonyms (human)	GRL
Gene (mouse)	Nr3c1
Gene synonyms (mouse)	Grl, Grl1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	15
Consensus	RGdACAnAvWGThCY
GC content	47.1%
Information content (bits; total / per base)	13.476 / 0.898
Data sources	ChIP-Seq + HT-SELEX
Aligned words	838

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	82 (479)	0.871	0.967	0.816	0.945	0.856	0.958	3.638	5.23	202.284	872.854
Mouse	93 (512)	0.828	0.991	0.777	0.982	0.827	0.992	3.453	6.36	184.431	734.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.759	0.771	0.628	0.646	0.568	0.586
Non-Methyl HT-SELEX, 2 experiments	best	0.832	0.844	0.664	0.688	0.585	0.61

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.464	14.738	0.167	0.067

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	Steroid hormone receptors {2.1.1} (TFClass)
TF subfamily	GR-like (NR3C) {2.1.1.1} (TFClass)
TFClass ID	TFClass: 2.1.1.1.1
HGNC	HGNC:7978
MGI	MGI:95824
EntrezGene (human)	GeneID:2908 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	GCR_HUMAN
UniProt ID (mouse)	GCR_MOUSE
UniProt AC (human)	P04150 (TFClass)
UniProt AC (mouse)	P06537 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	82 human, 93 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

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

PCM

	A	C	G	T
01	380.0	12.0	350.0	96.0
02	72.0	9.0	712.0	45.0
03	341.0	114.0	203.0	180.0
04	776.0	18.0	17.0	27.0
05	7.0	815.0	9.0	7.0
06	680.0	23.0	48.0	87.0
07	202.0	190.0	296.0	150.0
08	504.0	0.0	334.0	0.0
09	364.0	200.0	192.0	82.0
10	115.0	80.0	21.0	622.0
11	11.0	2.0	824.0	1.0
12	29.0	16.0	10.0	783.0
13	166.0	191.0	131.0	350.0
14	37.0	712.0	11.0	78.0
15	71.0	363.0	18.0	386.0

PFM

	A	C	G	T
01	0.453	0.014	0.418	0.115
02	0.086	0.011	0.85	0.054
03	0.407	0.136	0.242	0.215
04	0.926	0.021	0.02	0.032
05	0.008	0.973	0.011	0.008
06	0.811	0.027	0.057	0.104
07	0.241	0.227	0.353	0.179
08	0.601	0.0	0.399	0.0
09	0.434	0.239	0.229	0.098
10	0.137	0.095	0.025	0.742
11	0.013	0.002	0.983	0.001
12	0.035	0.019	0.012	0.934
13	0.198	0.228	0.156	0.418
14	0.044	0.85	0.013	0.093
15	0.085	0.433	0.021	0.461

PWM

	A	C	G	T
01	0.592	-2.737	0.51	-0.771
02	-1.053	-2.984	1.218	-1.509
03	0.484	-0.602	-0.031	-0.15
04	1.304	-2.373	-2.425	-1.996
05	-3.191	1.353	-2.984	-3.191
06	1.172	-2.147	-1.447	-0.868
07	-0.036	-0.097	0.343	-0.331
08	0.873	-4.832	0.463	-4.832
09	0.549	-0.046	-0.087	-0.926
10	-0.593	-0.95	-2.231	1.083
11	-2.812	-4.049	1.363	-4.366
12	-1.929	-2.48	-2.895	1.313
13	-0.231	-0.092	-0.465	0.51
14	-1.697	1.218	-2.812	-0.975
15	-1.067	0.546	-2.373	0.607

Standard thresholds

P-value	Threshold
0.001	3.63066
0.0005	4.70941
0.0001	6.94061