GCM2.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GCM2.H12INVITRO.0.SM.B
Gene (human)	GCM2 (GeneCards)
Gene synonyms (human)	GCMB
Gene (mouse)	Gcm2
Gene synonyms (mouse)	Gcmb
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	10
Consensus	nRCCCGCATn
GC content	62.55%
Information content (bits; total / per base)	13.181 / 1.318
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	6405

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.97	0.956	0.879	0.861	0.789	0.777
Overall, 4 experiments	best	0.992	0.987	0.987	0.979	0.959	0.948
Methyl HT-SELEX, 1 experiments	median	0.954	0.933	0.878	0.849	0.858	0.811
Methyl HT-SELEX, 1 experiments	best	0.954	0.933	0.878	0.849	0.858	0.811
Non-Methyl HT-SELEX, 3 experiments	median	0.986	0.979	0.88	0.873	0.72	0.742
Non-Methyl HT-SELEX, 3 experiments	best	0.992	0.987	0.987	0.979	0.959	0.948

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.918	0.742	0.894	0.558
batch 2	0.815	0.614	0.798	0.539

TF superclass	beta-Hairpin exposed by an alpha/beta-scaffold {7} (TFClass)
TF class	GCM domain factors {7.2} (TFClass)
TF family	GCM {7.2.1} (TFClass)
TF subfamily	{7.2.1.0} (TFClass)
TFClass ID	TFClass: 7.2.1.0.2
HGNC	HGNC:4198
MGI	MGI:1861438
EntrezGene (human)	GeneID:9247 (SSTAR profile)
EntrezGene (mouse)	GeneID:107889 (SSTAR profile)
UniProt ID (human)	GCM2_HUMAN
UniProt ID (mouse)	GCM2_MOUSE
UniProt AC (human)	O75603 (TFClass)
UniProt AC (mouse)	O09102 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	GCM2.H12INVITRO.0.SM.B.pcm
PWM	GCM2.H12INVITRO.0.SM.B.pwm
PFM	GCM2.H12INVITRO.0.SM.B.pfm
Alignment	GCM2.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	GCM2.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	GCM2.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	GCM2.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	GCM2.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	GCM2.H12INVITRO.0.SM.B_homer_format_0.001.txt GCM2.H12INVITRO.0.SM.B_homer_format_0.0005.txt GCM2.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1659.75	1849.75	948.75	1946.75
02	4300.25	367.25	1226.25	511.25
03	0.0	6405.0	0.0	0.0
04	0.0	6405.0	0.0	0.0
05	0.0	6405.0	0.0	0.0
06	0.0	0.0	6405.0	0.0
07	0.0	5662.0	0.0	743.0
08	6405.0	0.0	0.0	0.0
09	187.0	795.0	300.0	5123.0
10	1781.75	1690.75	1604.75	1327.75

PFM

	A	C	G	T
01	0.259	0.289	0.148	0.304
02	0.671	0.057	0.191	0.08
03	0.0	1.0	0.0	0.0
04	0.0	1.0	0.0	0.0
05	0.0	1.0	0.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.884	0.0	0.116
08	1.0	0.0	0.0	0.0
09	0.029	0.124	0.047	0.8
10	0.278	0.264	0.251	0.207

PWM

	A	C	G	T
01	0.036	0.144	-0.522	0.195
02	0.987	-1.468	-0.266	-1.139
03	-6.595	1.385	-6.595	-6.595
04	-6.595	1.385	-6.595	-6.595
05	-6.595	1.385	-6.595	-6.595
06	-6.595	-6.595	1.385	-6.595
07	-6.595	1.262	-6.595	-0.766
08	1.385	-6.595	-6.595	-6.595
09	-2.137	-0.699	-1.669	1.162
10	0.107	0.054	0.002	-0.187

Standard thresholds

P-value	Threshold
0.001	0.720905
0.0005	2.616335
0.0001	7.470405