GCR.H13RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GCR.H13RSNP.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	GnACWbbbTGThCYh
GC content	48.59%
Information content (bits; total / per base)	14.056 / 0.937
Data sources	ChIP-Seq + HT-SELEX
Aligned words	794
Previous names	GCR.H12RSNP.0.PS.A

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)	0.866	0.962	0.811	0.933	0.838	0.945	3.468	5.078	195.456	848.553
Mouse	93 (512)	0.827	0.986	0.772	0.97	0.81	0.988	3.278	6.045	181.682	731.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.761	0.771	0.628	0.646	0.567	0.586
Non-Methyl HT-SELEX, 2 experiments	best	0.834	0.845	0.665	0.688	0.585	0.611

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.799	18.387	0.173	0.072

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	GCR.H13RSNP.0.PS.A.pcm
PWM	GCR.H13RSNP.0.PS.A.pwm
PFM	GCR.H13RSNP.0.PS.A.pfm
Threshold to P-value map	GCR.H13RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	GCR.H13RSNP.0.PS.A_jaspar_format.txt
MEME format	GCR.H13RSNP.0.PS.A_meme_format.meme
Transfac format	GCR.H13RSNP.0.PS.A_transfac_format.txt
Homer format	GCR.H13RSNP.0.PS.A_homer_format_0.001.txt GCR.H13RSNP.0.PS.A_homer_format_0.0005.txt GCR.H13RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	41.0	3.0	729.0	21.0
02	302.0	125.0	183.0	184.0
03	754.0	5.0	9.0	26.0
04	1.0	786.0	1.0	6.0
05	566.0	17.0	60.0	151.0
06	51.0	252.0	93.0	398.0
07	109.0	160.0	142.0	383.0
08	91.0	369.0	172.0	162.0
09	46.0	54.0	11.0	683.0
10	12.0	16.0	766.0	0.0
11	7.0	13.0	8.0	766.0
12	119.0	198.0	70.0	407.0
13	14.0	729.0	3.0	48.0
14	20.0	411.0	5.0	358.0
15	140.0	284.0	113.0	257.0

PFM

	A	C	G	T
01	0.052	0.004	0.918	0.026
02	0.38	0.157	0.23	0.232
03	0.95	0.006	0.011	0.033
04	0.001	0.99	0.001	0.008
05	0.713	0.021	0.076	0.19
06	0.064	0.317	0.117	0.501
07	0.137	0.202	0.179	0.482
08	0.115	0.465	0.217	0.204
09	0.058	0.068	0.014	0.86
10	0.015	0.02	0.965	0.0
11	0.009	0.016	0.01	0.965
12	0.15	0.249	0.088	0.513
13	0.018	0.918	0.004	0.06
14	0.025	0.518	0.006	0.451
15	0.176	0.358	0.142	0.324

PWM

	A	C	G	T
01	-1.546	-3.758	1.295	-2.178
02	0.417	-0.458	-0.081	-0.075
03	1.328	-3.402	-2.932	-1.979
04	-4.317	1.37	-4.317	-3.262
05	1.042	-2.372	-1.177	-0.271
06	-1.335	0.237	-0.749	0.691
07	-0.593	-0.214	-0.332	0.653
08	-0.77	0.616	-0.142	-0.201
09	-1.435	-1.28	-2.76	1.23
10	-2.684	-2.427	1.344	-4.787
11	-3.139	-2.613	-3.03	1.344
12	-0.506	-0.003	-1.027	0.714
13	-2.547	1.295	-3.758	-1.394
14	-2.223	0.723	-3.402	0.586
15	-0.346	0.356	-0.557	0.256

Standard thresholds

P-value	Threshold
0.001	3.32246
0.0005	4.45466
0.0001	6.82356