GCR.H12RSNP.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GCR.H12RSNP.1.S.B
Gene (human)	NR3C1 (GeneCards)
Gene synonyms (human)	GRL
Gene (mouse)	Nr3c1
Gene synonyms (mouse)	Grl, Grl1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	9
Consensus	nvTGTWCbn
GC content	45.4%
Information content (bits; total / per base)	7.476 / 0.831
Data sources	HT-SELEX
Aligned words	8247

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)	0.778	0.895	0.621	0.794	0.714	0.799	1.783	2.089	74.222	227.523
Mouse	93 (512)	0.737	0.83	0.571	0.7	0.701	0.796	1.714	2.077	68.128	238.301

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.756	0.723	0.653	0.639	0.587	0.588
Non-Methyl HT-SELEX, 2 experiments	best	0.819	0.794	0.687	0.68	0.605	0.612

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.75	17.745	0.131	0.055

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.H12RSNP.1.S.B.pcm
PWM	GCR.H12RSNP.1.S.B.pwm
PFM	GCR.H12RSNP.1.S.B.pfm
Alignment	GCR.H12RSNP.1.S.B.words.tsv
Threshold to P-value map	GCR.H12RSNP.1.S.B.thr
Motif in other formats
JASPAR format	GCR.H12RSNP.1.S.B_jaspar_format.txt
MEME format	GCR.H12RSNP.1.S.B_meme_format.meme
Transfac format	GCR.H12RSNP.1.S.B_transfac_format.txt
Homer format	GCR.H12RSNP.1.S.B_homer_format_0.001.txt GCR.H12RSNP.1.S.B_homer_format_0.0005.txt GCR.H12RSNP.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2506.25	2146.25	1494.25	2100.25
02	3831.25	1218.25	2376.25	821.25
03	573.0	938.0	119.0	6617.0
04	0.0	1.0	8244.0	2.0
05	39.0	26.0	0.0	8182.0
06	2986.0	638.0	266.0	4357.0
07	119.0	7581.0	43.0	504.0
08	777.25	3147.25	1331.25	2991.25
09	1589.0	2311.0	1815.0	2532.0

PFM

	A	C	G	T
01	0.304	0.26	0.181	0.255
02	0.465	0.148	0.288	0.1
03	0.069	0.114	0.014	0.802
04	0.0	0.0	1.0	0.0
05	0.005	0.003	0.0	0.992
06	0.362	0.077	0.032	0.528
07	0.014	0.919	0.005	0.061
08	0.094	0.382	0.161	0.363
09	0.193	0.28	0.22	0.307

PWM

	A	C	G	T
01	0.195	0.04	-0.322	0.018
02	0.619	-0.525	0.142	-0.919
03	-1.278	-0.786	-2.835	1.165
04	-6.82	-6.452	1.385	-6.184
05	-3.913	-4.291	-6.82	1.378
06	0.37	-1.171	-2.04	0.748
07	-2.835	1.301	-3.82	-1.405
08	-0.974	0.423	-0.437	0.372
09	-0.26	0.114	-0.127	0.205

Standard thresholds

P-value	Threshold
0.001	5.408185
0.0005	6.045875
0.0001	6.874235