TFCP2.H12INVIVO.2.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TFCP2.H12INVIVO.2.S.D
Gene (human)	TFCP2 (GeneCards)
Gene synonyms (human)	LSF, SEF
Gene (mouse)	Tfcp2
Gene synonyms (mouse)	Tcfcp2
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	D

Motif length	13
Consensus	nWdAACCGGWWhn
GC content	46.52%
Information content (bits; total / per base)	13.555 / 1.043
Data sources	HT-SELEX
Aligned words	2475

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.936	0.902	0.891	0.851	0.823	0.787
Overall, 5 experiments	best	0.984	0.972	0.974	0.959	0.958	0.937
Methyl HT-SELEX, 2 experiments	median	0.958	0.934	0.93	0.901	0.886	0.856
Methyl HT-SELEX, 2 experiments	best	0.98	0.965	0.969	0.951	0.948	0.924
Non-Methyl HT-SELEX, 3 experiments	median	0.829	0.788	0.699	0.684	0.603	0.613
Non-Methyl HT-SELEX, 3 experiments	best	0.984	0.972	0.974	0.959	0.958	0.937

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.768	0.511	0.735	0.486
batch 2	0.646	0.15	0.704	0.462

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	Grainyhead domain factors {6.7} (TFClass)
TF family	CP2-related {6.7.2} (TFClass)
TF subfamily	{6.7.2.0} (TFClass)
TFClass ID	TFClass: 6.7.2.0.1
HGNC	HGNC:11748
MGI	MGI:98509
EntrezGene (human)	GeneID:7024 (SSTAR profile)
EntrezGene (mouse)	GeneID:21422 (SSTAR profile)
UniProt ID (human)	TFCP2_HUMAN
UniProt ID (mouse)	TFCP2_MOUSE
UniProt AC (human)	Q12800 (TFClass)
UniProt AC (mouse)	Q9ERA0 (TFClass)
GRECO-DB-TF	yes

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

PCM	TFCP2.H12INVIVO.2.S.D.pcm
PWM	TFCP2.H12INVIVO.2.S.D.pwm
PFM	TFCP2.H12INVIVO.2.S.D.pfm
Alignment	TFCP2.H12INVIVO.2.S.D.words.tsv
Threshold to P-value map	TFCP2.H12INVIVO.2.S.D.thr
Motif in other formats
JASPAR format	TFCP2.H12INVIVO.2.S.D_jaspar_format.txt
MEME format	TFCP2.H12INVIVO.2.S.D_meme_format.meme
Transfac format	TFCP2.H12INVIVO.2.S.D_transfac_format.txt
Homer format	TFCP2.H12INVIVO.2.S.D_homer_format_0.001.txt TFCP2.H12INVIVO.2.S.D_homer_format_0.0005.txt TFCP2.H12INVIVO.2.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	582.5	530.5	604.5	757.5
02	1664.5	211.5	274.5	324.5
03	1231.0	224.0	664.0	356.0
04	2422.0	11.0	9.0	33.0
05	2388.0	0.0	0.0	87.0
06	0.0	2475.0	0.0	0.0
07	0.0	2416.0	0.0	59.0
08	76.0	0.0	2399.0	0.0
09	0.0	7.0	2468.0	0.0
10	878.0	111.0	9.0	1477.0
11	530.0	317.0	112.0	1516.0
12	505.5	784.5	273.5	911.5
13	572.5	673.5	393.5	835.5

PFM

	A	C	G	T
01	0.235	0.214	0.244	0.306
02	0.673	0.085	0.111	0.131
03	0.497	0.091	0.268	0.144
04	0.979	0.004	0.004	0.013
05	0.965	0.0	0.0	0.035
06	0.0	1.0	0.0	0.0
07	0.0	0.976	0.0	0.024
08	0.031	0.0	0.969	0.0
09	0.0	0.003	0.997	0.0
10	0.355	0.045	0.004	0.597
11	0.214	0.128	0.045	0.613
12	0.204	0.317	0.111	0.368
13	0.231	0.272	0.159	0.338

PWM

	A	C	G	T
01	-0.06	-0.153	-0.023	0.202
02	0.988	-1.067	-0.809	-0.643
03	0.686	-1.011	0.07	-0.55
04	1.362	-3.869	-4.037	-2.877
05	1.348	-5.761	-5.761	-1.943
06	-5.761	1.384	-5.761	-5.761
07	-5.761	1.36	-5.761	-2.321
08	-2.075	-5.761	1.353	-5.761
09	-5.761	-4.239	1.381	-5.761
10	0.349	-1.704	-4.037	0.868
11	-0.154	-0.666	-1.695	0.894
12	-0.201	0.237	-0.812	0.386
13	-0.077	0.085	-0.451	0.3

Standard thresholds

P-value	Threshold
0.001	2.68621
0.0005	4.07546
0.0001	7.069385