GRHL1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GRHL1.H12INVITRO.0.PSM.A
Gene (human)	GRHL1 (GeneCards)
Gene synonyms (human)	LBP32, MGR, TFCP2L2
Gene (mouse)	Grhl1
Gene synonyms (mouse)	Mgr, Tcfcp2l2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	19
Consensus	ndAACCKGTWhdWChdGhh
GC content	46.45%
Information content (bits; total / per base)	16.271 / 0.856
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9105

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	3 (20)	0.966	0.975	0.935	0.952	0.945	0.958	4.499	4.869	521.263	712.081

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.999	0.999	0.996	0.994	0.948	0.95
Overall, 8 experiments	best	1.0	1.0	1.0	0.999	0.997	0.996
Methyl HT-SELEX, 2 experiments	median	1.0	0.999	0.999	0.998	0.996	0.994
Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.999	0.996	0.995
Non-Methyl HT-SELEX, 6 experiments	median	0.991	0.988	0.937	0.933	0.814	0.826
Non-Methyl HT-SELEX, 6 experiments	best	1.0	1.0	1.0	0.999	0.997	0.996

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.892	0.665	0.872	0.583

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	Grainyhead domain factors {6.7} (TFClass)
TF family	Grainyhead-related {6.7.1} (TFClass)
TF subfamily	GRH-like {6.7.1.1} (TFClass)
TFClass ID	TFClass: 6.7.1.1.1
HGNC	HGNC:17923
MGI	MGI:2182540
EntrezGene (human)	GeneID:29841 (SSTAR profile)
EntrezGene (mouse)	GeneID:195733 (SSTAR profile)
UniProt ID (human)	GRHL1_HUMAN
UniProt ID (mouse)	GRHL1_MOUSE
UniProt AC (human)	Q9NZI5 (TFClass)
UniProt AC (mouse)	Q921D9 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	GRHL1.H12INVITRO.0.PSM.A.pcm
PWM	GRHL1.H12INVITRO.0.PSM.A.pwm
PFM	GRHL1.H12INVITRO.0.PSM.A.pfm
Alignment	GRHL1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	GRHL1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	GRHL1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	GRHL1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	GRHL1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	GRHL1.H12INVITRO.0.PSM.A_homer_format_0.001.txt GRHL1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt GRHL1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3233.75	2219.75	1807.75	1843.75
02	4979.5	759.5	1914.5	1451.5
03	8161.0	47.0	494.0	403.0
04	8767.0	10.0	37.0	291.0
05	0.0	9100.0	4.0	1.0
06	1130.0	7320.0	33.0	622.0
07	951.0	76.0	6992.0	1086.0
08	6.0	3.0	9096.0	0.0
09	1293.0	274.0	38.0	7500.0
10	1774.0	999.0	118.0	6214.0
11	3288.0	1028.0	750.0	4039.0
12	4356.0	565.0	1596.0	2588.0
13	5428.0	310.0	1329.0	2038.0
14	120.0	8600.0	137.0	248.0
15	2041.0	4185.0	1229.0	1650.0
16	3097.0	677.0	3977.0	1354.0
17	141.0	718.0	8134.0	112.0
18	2129.0	1516.0	1039.0	4421.0
19	2096.75	1925.75	1292.75	3789.75

PFM

	A	C	G	T
01	0.355	0.244	0.199	0.202
02	0.547	0.083	0.21	0.159
03	0.896	0.005	0.054	0.044
04	0.963	0.001	0.004	0.032
05	0.0	0.999	0.0	0.0
06	0.124	0.804	0.004	0.068
07	0.104	0.008	0.768	0.119
08	0.001	0.0	0.999	0.0
09	0.142	0.03	0.004	0.824
10	0.195	0.11	0.013	0.682
11	0.361	0.113	0.082	0.444
12	0.478	0.062	0.175	0.284
13	0.596	0.034	0.146	0.224
14	0.013	0.945	0.015	0.027
15	0.224	0.46	0.135	0.181
16	0.34	0.074	0.437	0.149
17	0.015	0.079	0.893	0.012
18	0.234	0.167	0.114	0.486
19	0.23	0.212	0.142	0.416

PWM

	A	C	G	T
01	0.351	-0.025	-0.23	-0.21
02	0.782	-1.096	-0.173	-0.449
03	1.276	-3.834	-1.524	-1.727
04	1.348	-5.223	-4.061	-2.05
05	-6.907	1.385	-5.894	-6.544
06	-0.699	1.167	-4.168	-1.295
07	-0.871	-3.371	1.122	-0.739
08	-5.618	-6.068	1.385	-6.907
09	-0.565	-2.11	-4.035	1.192
10	-0.249	-0.822	-2.941	1.004
11	0.367	-0.794	-1.108	0.573
12	0.649	-1.39	-0.355	0.128
13	0.868	-1.987	-0.537	-0.11
14	-2.925	1.328	-2.795	-2.209
15	-0.109	0.609	-0.615	-0.321
16	0.308	-1.21	0.558	-0.519
17	-2.766	-1.152	1.273	-2.993
18	-0.067	-0.406	-0.783	0.663
19	-0.082	-0.167	-0.565	0.509

Standard thresholds

P-value	Threshold
0.001	1.92876
0.0005	3.30806
0.0001	6.11476