TFCP2.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TFCP2.H12INVITRO.1.SM.B
Gene (human)	TFCP2 (GeneCards)
Gene synonyms (human)	LSF, SEF
Gene (mouse)	Tfcp2
Gene synonyms (mouse)	Tcfcp2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	20
Consensus	nddCYRGhhndWACCGGWhn
GC content	50.36%
Information content (bits; total / per base)	14.993 / 0.75
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9816

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.992	0.987	0.976	0.967	0.928	0.914
Overall, 5 experiments	best	1.0	0.999	0.999	0.999	0.997	0.996
Methyl HT-SELEX, 2 experiments	median	0.996	0.993	0.988	0.982	0.962	0.954
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.999	0.998	0.996	0.995
Non-Methyl HT-SELEX, 3 experiments	median	0.96	0.953	0.78	0.792	0.635	0.672
Non-Methyl HT-SELEX, 3 experiments	best	1.0	0.999	0.999	0.999	0.997	0.996

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.902	0.752	0.885	0.588
batch 2	0.707	0.196	0.767	0.525

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.H12INVITRO.1.SM.B.pcm
PWM	TFCP2.H12INVITRO.1.SM.B.pwm
PFM	TFCP2.H12INVITRO.1.SM.B.pfm
Alignment	TFCP2.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	TFCP2.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	TFCP2.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	TFCP2.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	TFCP2.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	TFCP2.H12INVITRO.1.SM.B_homer_format_0.001.txt TFCP2.H12INVITRO.1.SM.B_homer_format_0.0005.txt TFCP2.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3294.25	1905.25	2589.25	2027.25
02	5663.25	758.25	1646.25	1748.25
03	5061.0	312.0	1822.0	2621.0
04	63.0	8837.0	676.0	240.0
05	618.0	6134.0	303.0	2761.0
06	3080.0	309.0	5812.0	615.0
07	250.0	810.0	8689.0	67.0
08	2737.0	2593.0	279.0	4207.0
09	1710.0	2421.0	902.0	4783.0
10	2226.0	2271.0	2060.0	3259.0
11	4354.0	779.0	3237.0	1446.0
12	7480.0	145.0	821.0	1370.0
13	7552.0	5.0	108.0	2151.0
14	1.0	9809.0	6.0	0.0
15	35.0	7795.0	13.0	1973.0
16	2189.0	0.0	7572.0	55.0
17	8.0	288.0	9519.0	1.0
18	3075.0	962.0	50.0	5729.0
19	2198.5	1700.5	652.5	5264.5
20	2348.0	2581.0	1695.0	3192.0

PFM

	A	C	G	T
01	0.336	0.194	0.264	0.207
02	0.577	0.077	0.168	0.178
03	0.516	0.032	0.186	0.267
04	0.006	0.9	0.069	0.024
05	0.063	0.625	0.031	0.281
06	0.314	0.031	0.592	0.063
07	0.025	0.083	0.885	0.007
08	0.279	0.264	0.028	0.429
09	0.174	0.247	0.092	0.487
10	0.227	0.231	0.21	0.332
11	0.444	0.079	0.33	0.147
12	0.762	0.015	0.084	0.14
13	0.769	0.001	0.011	0.219
14	0.0	0.999	0.001	0.0
15	0.004	0.794	0.001	0.201
16	0.223	0.0	0.771	0.006
17	0.001	0.029	0.97	0.0
18	0.313	0.098	0.005	0.584
19	0.224	0.173	0.066	0.536
20	0.239	0.263	0.173	0.325

PWM

	A	C	G	T
01	0.294	-0.253	0.054	-0.191
02	0.836	-1.172	-0.399	-0.339
03	0.723	-2.056	-0.297	0.066
04	-3.627	1.281	-1.287	-2.316
05	-1.376	0.916	-2.085	0.118
06	0.227	-2.066	0.862	-1.381
07	-2.276	-1.107	1.264	-3.568
08	0.109	0.055	-2.167	0.539
09	-0.361	-0.014	-0.999	0.667
10	-0.097	-0.077	-0.175	0.283
11	0.573	-1.145	0.277	-0.528
12	1.114	-2.814	-1.093	-0.582
13	1.123	-5.819	-3.103	-0.132
14	-6.613	1.385	-5.69	-6.974
15	-4.187	1.155	-5.079	-0.218
16	-0.114	-6.974	1.126	-3.758
17	-5.474	-2.136	1.355	-6.613
18	0.225	-0.935	-3.849	0.847
19	-0.11	-0.366	-1.322	0.763
20	-0.044	0.05	-0.37	0.263

Standard thresholds

P-value	Threshold
0.001	2.60546
0.0005	3.92531
0.0001	6.56921