GCR.H12INVIVO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GCR.H12INVIVO.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	ndTGTWCbn
GC content	44.56%
Information content (bits; total / per base)	8.056 / 0.895
Data sources	HT-SELEX
Aligned words	9505

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)	0.777	0.889	0.62	0.789	0.712	0.799	1.777	2.083	72.347	228.854
Mouse	93 (512)	0.741	0.83	0.573	0.699	0.701	0.788	1.7	2.068	69.482	245.102

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.758	0.725	0.654	0.641	0.587	0.589
Non-Methyl HT-SELEX, 2 experiments	best	0.821	0.798	0.688	0.682	0.605	0.613

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.56	15.581	0.128	0.052

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.1.S.B.pcm
PWM	GCR.H12INVIVO.1.S.B.pwm
PFM	GCR.H12INVIVO.1.S.B.pfm
Alignment	GCR.H12INVIVO.1.S.B.words.tsv
Threshold to P-value map	GCR.H12INVIVO.1.S.B.thr
Motif in other formats
JASPAR format	GCR.H12INVIVO.1.S.B_jaspar_format.txt
MEME format	GCR.H12INVIVO.1.S.B_meme_format.meme
Transfac format	GCR.H12INVIVO.1.S.B_transfac_format.txt
Homer format	GCR.H12INVIVO.1.S.B_homer_format_0.001.txt GCR.H12INVIVO.1.S.B_homer_format_0.0005.txt GCR.H12INVIVO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2962.25	2389.25	1675.25	2478.25
02	4323.75	1243.75	2430.75	1506.75
03	350.0	638.0	149.0	8368.0
04	0.0	8.0	9486.0	11.0
05	21.0	36.0	0.0	9448.0
06	3633.0	809.0	152.0	4911.0
07	65.0	9174.0	38.0	228.0
08	757.25	3908.25	1152.25	3687.25
09	1810.25	2711.25	2115.25	2868.25

PFM

	A	C	G	T
01	0.312	0.251	0.176	0.261
02	0.455	0.131	0.256	0.159
03	0.037	0.067	0.016	0.88
04	0.0	0.001	0.998	0.001
05	0.002	0.004	0.0	0.994
06	0.382	0.085	0.016	0.517
07	0.007	0.965	0.004	0.024
08	0.08	0.411	0.121	0.388
09	0.19	0.285	0.223	0.302

PWM

	A	C	G	T
01	0.22	0.005	-0.349	0.042
02	0.598	-0.647	0.023	-0.455
03	-1.91	-1.312	-2.755	1.258
04	-6.946	-5.443	1.384	-5.187
05	-4.626	-4.129	-6.946	1.38
06	0.424	-1.076	-2.735	0.725
07	-3.565	1.35	-4.078	-2.335
08	-1.142	0.497	-0.723	0.439
09	-0.272	0.132	-0.116	0.188

Standard thresholds

P-value	Threshold
0.001	5.59821
0.0005	6.19586
0.0001	7.04754